From c1ea4c9f3a26fba718e78697edd90941939b9469 Mon Sep 17 00:00:00 2001
From: Laura Cook <l.cook2@student.unimelb.edu.au>
Date: Fri, 11 Dec 2020 12:37:18 +1100
Subject: [PATCH] first commit

---
 cross_species_comparison/README.md            |   7 +-
 .../scripts/axtChain_commands.sh              | 718 +++++++++++++++++
 .../scripts/chainSort_commands.sh             | 713 +++++++++++++++++
 cross_species_comparison/scripts/lastz.sh     |   7 +-
 .../scripts/lastz_commands.sh                 | 718 +++++++++++++++++
 .../scripts/maf-convert_commands.sh           | 718 +++++++++++++++++
 .../scripts/repeatMaskerCommands.sh           | 719 ++++++++++++++++++
 mouse/README.md                               |  24 +-
 8 files changed, 3599 insertions(+), 25 deletions(-)
 create mode 100644 cross_species_comparison/scripts/axtChain_commands.sh
 create mode 100644 cross_species_comparison/scripts/chainSort_commands.sh
 create mode 100644 cross_species_comparison/scripts/lastz_commands.sh
 create mode 100644 cross_species_comparison/scripts/maf-convert_commands.sh
 create mode 100644 cross_species_comparison/scripts/repeatMaskerCommands.sh

diff --git a/cross_species_comparison/README.md b/cross_species_comparison/README.md
index 1b63dab..a3ea164 100644
--- a/cross_species_comparison/README.md
+++ b/cross_species_comparison/README.md
@@ -283,7 +283,8 @@ https://github.com/josiahseaman/FluentDNA
 
 
 
-References
+### References
+
 [1] Sharma V, Hiller M. Increased alignment sensitivity improves the usage of genome alignments for comparative gene annotation. Nucleic Acids Res., 45(14), 8369–8377, 2017
 
 [2] Suarez H, Langer BE, Ladde P, Hiller M. chainCleaner improves genome alignment specificity and sensitivity. Bioinformatics, 33(11):1596-1603, 2017
@@ -293,3 +294,7 @@ References
 [4] Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. PNAS, 100(20):11484-9, 2003
 
 [5] Osipova E, Hecker N, Hiller M. RepeatFiller newly identifies megabases of aligning repetitive sequences and improves annotations of conserved non-exonic elements, submitted
+
+[6] FluentDNA paper
+
+[7] Kent tools UCSC
\ No newline at end of file
diff --git a/cross_species_comparison/scripts/axtChain_commands.sh b/cross_species_comparison/scripts/axtChain_commands.sh
new file mode 100644
index 0000000..27f4552
--- /dev/null
+++ b/cross_species_comparison/scripts/axtChain_commands.sh
@@ -0,0 +1,718 @@
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+axtChain -linearGap=loose /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/axt/scaffold00713_pilon_pilon_mm10.smiCra1.axt /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.2bit /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.2bit scaffold00713_pilon_pilon_mm10.smiCra1.chain
+axtChain -linearGap=loose /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/axt/scaffold00714_pilon_pilon_mm10.smiCra1.axt /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.2bit /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.2bit scaffold00714_pilon_pilon_mm10.smiCra1.chain
+axtChain -linearGap=loose /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/axt/scaffold00715_pilon_pilon_mm10.smiCra1.axt /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.2bit /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.2bit scaffold00715_pilon_pilon_mm10.smiCra1.chain
+axtChain -linearGap=loose /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/axt/scaffold00716_pilon_pilon_mm10.smiCra1.axt /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.2bit /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.2bit scaffold00716_pilon_pilon_mm10.smiCra1.chain
+axtChain -linearGap=loose /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/axt/scaffold00717_pilon_pilon_mm10.smiCra1.axt /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.2bit /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.2bit scaffold00717_pilon_pilon_mm10.smiCra1.chain
+axtChain -linearGap=loose /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/axt/scaffold00718_pilon_pilon_mm10.smiCra1.axt /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.2bit /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.2bit scaffold00718_pilon_pilon_mm10.smiCra1.chain
+axtChain -linearGap=loose /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/axt/scaffold00719_pilon_pilon_mm10.smiCra1.axt /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.2bit /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.2bit scaffold00719_pilon_pilon_mm10.smiCra1.chain
diff --git a/cross_species_comparison/scripts/chainSort_commands.sh b/cross_species_comparison/scripts/chainSort_commands.sh
new file mode 100644
index 0000000..5964d5f
--- /dev/null
+++ b/cross_species_comparison/scripts/chainSort_commands.sh
@@ -0,0 +1,713 @@
+chainSort scaffold00001_pilon_pilon_mm10.smiCra1.chain > scaffold00001_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00002_pilon_pilon_mm10.smiCra1.chain > scaffold00002_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00003_pilon_pilon_mm10.smiCra1.chain > scaffold00003_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00004_pilon_pilon_mm10.smiCra1.chain > scaffold00004_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00005_pilon_pilon_mm10.smiCra1.chain > scaffold00005_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00006_pilon_pilon_mm10.smiCra1.chain > scaffold00006_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00007_pilon_pilon_mm10.smiCra1.chain > scaffold00007_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00008_pilon_pilon_mm10.smiCra1.chain > scaffold00008_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00009_pilon_pilon_mm10.smiCra1.chain > scaffold00009_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00010_pilon_pilon_mm10.smiCra1.chain > scaffold00010_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00011_pilon_pilon_mm10.smiCra1.chain > scaffold00011_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00012_pilon_pilon_mm10.smiCra1.chain > scaffold00012_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00013_pilon_pilon_mm10.smiCra1.chain > scaffold00013_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00014_pilon_pilon_mm10.smiCra1.chain > scaffold00014_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00016_pilon_pilon_mm10.smiCra1.chain > scaffold00016_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00017_pilon_pilon_mm10.smiCra1.chain > scaffold00017_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00018_pilon_pilon_mm10.smiCra1.chain > scaffold00018_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00019_pilon_pilon_mm10.smiCra1.chain > scaffold00019_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00020_pilon_pilon_mm10.smiCra1.chain > scaffold00020_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00021_pilon_pilon_mm10.smiCra1.chain > scaffold00021_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00022_pilon_pilon_mm10.smiCra1.chain > scaffold00022_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00023_pilon_pilon_mm10.smiCra1.chain > scaffold00023_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00024_pilon_pilon_mm10.smiCra1.chain > scaffold00024_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00025_pilon_pilon_mm10.smiCra1.chain > scaffold00025_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00026_pilon_pilon_mm10.smiCra1.chain > scaffold00026_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00027_pilon_pilon_mm10.smiCra1.chain > scaffold00027_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00028_pilon_pilon_mm10.smiCra1.chain > scaffold00028_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00029_pilon_pilon_mm10.smiCra1.chain > scaffold00029_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00030_pilon_pilon_mm10.smiCra1.chain > scaffold00030_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00031_pilon_pilon_mm10.smiCra1.chain > scaffold00031_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00032_pilon_pilon_mm10.smiCra1.chain > scaffold00032_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00033_pilon_pilon_mm10.smiCra1.chain > scaffold00033_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00034_pilon_pilon_mm10.smiCra1.chain > scaffold00034_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00035_pilon_pilon_mm10.smiCra1.chain > scaffold00035_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00036_pilon_pilon_mm10.smiCra1.chain > scaffold00036_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00037_pilon_pilon_mm10.smiCra1.chain > scaffold00037_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00038_pilon_pilon_mm10.smiCra1.chain > scaffold00038_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00039_pilon_pilon_mm10.smiCra1.chain > scaffold00039_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00040_pilon_pilon_mm10.smiCra1.chain > scaffold00040_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00041_pilon_pilon_mm10.smiCra1.chain > scaffold00041_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00042_pilon_pilon_mm10.smiCra1.chain > scaffold00042_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00043_pilon_pilon_mm10.smiCra1.chain > scaffold00043_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00044_pilon_pilon_mm10.smiCra1.chain > scaffold00044_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00045_pilon_pilon_mm10.smiCra1.chain > scaffold00045_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00046_pilon_pilon_mm10.smiCra1.chain > scaffold00046_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00047_pilon_pilon_mm10.smiCra1.chain > scaffold00047_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00048_pilon_pilon_mm10.smiCra1.chain > scaffold00048_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00049_pilon_pilon_mm10.smiCra1.chain > scaffold00049_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00050_pilon_pilon_mm10.smiCra1.chain > scaffold00050_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00051_pilon_pilon_mm10.smiCra1.chain > scaffold00051_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00052_pilon_pilon_mm10.smiCra1.chain > scaffold00052_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00053_pilon_pilon_mm10.smiCra1.chain > scaffold00053_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00054_pilon_pilon_mm10.smiCra1.chain > scaffold00054_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00055_pilon_pilon_mm10.smiCra1.chain > scaffold00055_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00056_pilon_pilon_mm10.smiCra1.chain > scaffold00056_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00057_pilon_pilon_mm10.smiCra1.chain > scaffold00057_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00058_pilon_pilon_mm10.smiCra1.chain > scaffold00058_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00059_pilon_pilon_mm10.smiCra1.chain > scaffold00059_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00060_pilon_pilon_mm10.smiCra1.chain > scaffold00060_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00061_pilon_pilon_mm10.smiCra1.chain > scaffold00061_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00062_pilon_pilon_mm10.smiCra1.chain > scaffold00062_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00063_pilon_pilon_mm10.smiCra1.chain > scaffold00063_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00064_pilon_pilon_mm10.smiCra1.chain > scaffold00064_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00065_pilon_pilon_mm10.smiCra1.chain > scaffold00065_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00066_pilon_pilon_mm10.smiCra1.chain > scaffold00066_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00067_pilon_pilon_mm10.smiCra1.chain > scaffold00067_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00068_pilon_pilon_mm10.smiCra1.chain > scaffold00068_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00069_pilon_pilon_mm10.smiCra1.chain > scaffold00069_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00070_pilon_pilon_mm10.smiCra1.chain > scaffold00070_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00071_pilon_pilon_mm10.smiCra1.chain > scaffold00071_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00072_pilon_pilon_mm10.smiCra1.chain > scaffold00072_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00073_pilon_pilon_mm10.smiCra1.chain > scaffold00073_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00074_pilon_pilon_mm10.smiCra1.chain > scaffold00074_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00075_pilon_pilon_mm10.smiCra1.chain > scaffold00075_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00076_pilon_pilon_mm10.smiCra1.chain > scaffold00076_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00077_pilon_pilon_mm10.smiCra1.chain > scaffold00077_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00078_pilon_pilon_mm10.smiCra1.chain > scaffold00078_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00079_pilon_pilon_mm10.smiCra1.chain > scaffold00079_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00080_pilon_pilon_mm10.smiCra1.chain > scaffold00080_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00081_pilon_pilon_mm10.smiCra1.chain > scaffold00081_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00082_pilon_pilon_mm10.smiCra1.chain > scaffold00082_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00083_pilon_pilon_mm10.smiCra1.chain > scaffold00083_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00084_pilon_pilon_mm10.smiCra1.chain > scaffold00084_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00085_pilon_pilon_mm10.smiCra1.chain > scaffold00085_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00086_pilon_pilon_mm10.smiCra1.chain > scaffold00086_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00087_pilon_pilon_mm10.smiCra1.chain > scaffold00087_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00088_pilon_pilon_mm10.smiCra1.chain > scaffold00088_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00089_pilon_pilon_mm10.smiCra1.chain > scaffold00089_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00090_pilon_pilon_mm10.smiCra1.chain > scaffold00090_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00091_pilon_pilon_mm10.smiCra1.chain > scaffold00091_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00092_pilon_pilon_mm10.smiCra1.chain > scaffold00092_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00093_pilon_pilon_mm10.smiCra1.chain > scaffold00093_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00094_pilon_pilon_mm10.smiCra1.chain > scaffold00094_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00095_pilon_pilon_mm10.smiCra1.chain > scaffold00095_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00096_pilon_pilon_mm10.smiCra1.chain > scaffold00096_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00097_pilon_pilon_mm10.smiCra1.chain > scaffold00097_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00098_pilon_pilon_mm10.smiCra1.chain > scaffold00098_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00099_pilon_pilon_mm10.smiCra1.chain > scaffold00099_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00100_pilon_pilon_mm10.smiCra1.chain > scaffold00100_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00101_pilon_pilon_mm10.smiCra1.chain > scaffold00101_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00102_pilon_pilon_mm10.smiCra1.chain > scaffold00102_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00103_pilon_pilon_mm10.smiCra1.chain > scaffold00103_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00104_pilon_pilon_mm10.smiCra1.chain > scaffold00104_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00105_pilon_pilon_mm10.smiCra1.chain > scaffold00105_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00106_pilon_pilon_mm10.smiCra1.chain > scaffold00106_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00107_pilon_pilon_mm10.smiCra1.chain > scaffold00107_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00108_pilon_pilon_mm10.smiCra1.chain > scaffold00108_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00109_pilon_pilon_mm10.smiCra1.chain > scaffold00109_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00110_pilon_pilon_mm10.smiCra1.chain > scaffold00110_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00111_pilon_pilon_mm10.smiCra1.chain > scaffold00111_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00112_pilon_pilon_mm10.smiCra1.chain > scaffold00112_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00113_pilon_pilon_mm10.smiCra1.chain > scaffold00113_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00114_pilon_pilon_mm10.smiCra1.chain > scaffold00114_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00115_pilon_pilon_mm10.smiCra1.chain > scaffold00115_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00116_pilon_pilon_mm10.smiCra1.chain > scaffold00116_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00117_pilon_pilon_mm10.smiCra1.chain > scaffold00117_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00118_pilon_pilon_mm10.smiCra1.chain > scaffold00118_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00119_pilon_pilon_mm10.smiCra1.chain > scaffold00119_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00120_pilon_pilon_mm10.smiCra1.chain > scaffold00120_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00121_pilon_pilon_mm10.smiCra1.chain > scaffold00121_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00122_pilon_pilon_mm10.smiCra1.chain > scaffold00122_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00123_pilon_pilon_mm10.smiCra1.chain > scaffold00123_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00124_pilon_pilon_mm10.smiCra1.chain > scaffold00124_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00125_pilon_pilon_mm10.smiCra1.chain > scaffold00125_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00126_pilon_pilon_mm10.smiCra1.chain > scaffold00126_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00127_pilon_pilon_mm10.smiCra1.chain > scaffold00127_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00128_pilon_pilon_mm10.smiCra1.chain > scaffold00128_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00129_pilon_pilon_mm10.smiCra1.chain > scaffold00129_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00130_pilon_pilon_mm10.smiCra1.chain > scaffold00130_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00131_pilon_pilon_mm10.smiCra1.chain > scaffold00131_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00132_pilon_pilon_mm10.smiCra1.chain > scaffold00132_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00133_pilon_pilon_mm10.smiCra1.chain > scaffold00133_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00134_pilon_pilon_mm10.smiCra1.chain > scaffold00134_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00135_pilon_pilon_mm10.smiCra1.chain > scaffold00135_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00136_pilon_pilon_mm10.smiCra1.chain > scaffold00136_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00137_pilon_pilon_mm10.smiCra1.chain > scaffold00137_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00138_pilon_pilon_mm10.smiCra1.chain > scaffold00138_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00139_pilon_pilon_mm10.smiCra1.chain > scaffold00139_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00140_pilon_pilon_mm10.smiCra1.chain > scaffold00140_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00141_pilon_pilon_mm10.smiCra1.chain > scaffold00141_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00142_pilon_pilon_mm10.smiCra1.chain > scaffold00142_pilon_pilon_mm10.smiCra1.sorted.chain
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+chainSort scaffold00664_pilon_pilon_mm10.smiCra1.chain > scaffold00664_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00665_pilon_pilon_mm10.smiCra1.chain > scaffold00665_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00666_pilon_pilon_mm10.smiCra1.chain > scaffold00666_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00667_pilon_pilon_mm10.smiCra1.chain > scaffold00667_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00668_pilon_pilon_mm10.smiCra1.chain > scaffold00668_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00669_pilon_pilon_mm10.smiCra1.chain > scaffold00669_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00670_pilon_pilon_mm10.smiCra1.chain > scaffold00670_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00671_pilon_pilon_mm10.smiCra1.chain > scaffold00671_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00672_pilon_pilon_mm10.smiCra1.chain > scaffold00672_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00673_pilon_pilon_mm10.smiCra1.chain > scaffold00673_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00674_pilon_pilon_mm10.smiCra1.chain > scaffold00674_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00675_pilon_pilon_mm10.smiCra1.chain > scaffold00675_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00676_pilon_pilon_mm10.smiCra1.chain > scaffold00676_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00677_pilon_pilon_mm10.smiCra1.chain > scaffold00677_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00678_pilon_pilon_mm10.smiCra1.chain > scaffold00678_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00679_pilon_pilon_mm10.smiCra1.chain > scaffold00679_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00680_pilon_pilon_mm10.smiCra1.chain > scaffold00680_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00681_pilon_pilon_mm10.smiCra1.chain > scaffold00681_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00682_pilon_pilon_mm10.smiCra1.chain > scaffold00682_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00683_pilon_pilon_mm10.smiCra1.chain > scaffold00683_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00684_pilon_pilon_mm10.smiCra1.chain > scaffold00684_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00685_pilon_pilon_mm10.smiCra1.chain > scaffold00685_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00686_pilon_pilon_mm10.smiCra1.chain > scaffold00686_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00687_pilon_pilon_mm10.smiCra1.chain > scaffold00687_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00688_pilon_pilon_mm10.smiCra1.chain > scaffold00688_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00689_pilon_pilon_mm10.smiCra1.chain > scaffold00689_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00690_pilon_pilon_mm10.smiCra1.chain > scaffold00690_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00691_pilon_pilon_mm10.smiCra1.chain > scaffold00691_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00692_pilon_pilon_mm10.smiCra1.chain > scaffold00692_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00693_pilon_pilon_mm10.smiCra1.chain > scaffold00693_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00694_pilon_pilon_mm10.smiCra1.chain > scaffold00694_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00695_pilon_pilon_mm10.smiCra1.chain > scaffold00695_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00696_pilon_pilon_mm10.smiCra1.chain > scaffold00696_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00697_pilon_pilon_mm10.smiCra1.chain > scaffold00697_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00698_pilon_pilon_mm10.smiCra1.chain > scaffold00698_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00699_pilon_pilon_mm10.smiCra1.chain > scaffold00699_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00700_pilon_pilon_mm10.smiCra1.chain > scaffold00700_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00701_pilon_pilon_mm10.smiCra1.chain > scaffold00701_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00702_pilon_pilon_mm10.smiCra1.chain > scaffold00702_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00703_pilon_pilon_mm10.smiCra1.chain > scaffold00703_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00704_pilon_pilon_mm10.smiCra1.chain > scaffold00704_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00705_pilon_pilon_mm10.smiCra1.chain > scaffold00705_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00706_pilon_pilon_mm10.smiCra1.chain > scaffold00706_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00707_pilon_pilon_mm10.smiCra1.chain > scaffold00707_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00708_pilon_pilon_mm10.smiCra1.chain > scaffold00708_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00709_pilon_pilon_mm10.smiCra1.chain > scaffold00709_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00710_pilon_pilon_mm10.smiCra1.chain > scaffold00710_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00711_pilon_pilon_mm10.smiCra1.chain > scaffold00711_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00712_pilon_pilon_mm10.smiCra1.chain > scaffold00712_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00713_pilon_pilon_mm10.smiCra1.chain > scaffold00713_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00714_pilon_pilon_mm10.smiCra1.chain > scaffold00714_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00715_pilon_pilon_mm10.smiCra1.chain > scaffold00715_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00716_pilon_pilon_mm10.smiCra1.chain > scaffold00716_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00717_pilon_pilon_mm10.smiCra1.chain > scaffold00717_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00718_pilon_pilon_mm10.smiCra1.chain > scaffold00718_pilon_pilon_mm10.smiCra1.sorted.chain
+chainSort scaffold00719_pilon_pilon_mm10.smiCra1.chain > scaffold00719_pilon_pilon_mm10.smiCra1.sorted.chain
diff --git a/cross_species_comparison/scripts/lastz.sh b/cross_species_comparison/scripts/lastz.sh
index 480d56f..9017129 100644
--- a/cross_species_comparison/scripts/lastz.sh
+++ b/cross_species_comparison/scripts/lastz.sh
@@ -1,10 +1,10 @@
-##!/usr/bin/env bash
+#!/usr/bin/env bash
 
 ## This script loops through all scaffolds in the dunnart genome and
 ## generates a separate command for each scaffold
 ## These commands are then used in a slurm array script to run jobs in parallel
 
-TRA=($(for file in *.axt; do echo $file |cut -d "." -f 1-2;done))
+TRA=($(for file in *.chain; do echo $file |cut -d "." -f 1-2;done))
 
 echo ${TRA[@]}
 
@@ -19,7 +19,8 @@ do
 #echo 'maf-convert axt '${tr}.maf' > '${tr}.axt
 
 ## build co-linear alignment chains
-echo 'axtChain -linearGap=loose /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/axt/'${tr}'.axt /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.2bit /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.2bit '${tr}'.chain'
+#echo 'axtChain -linearGap=loose /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/axt/'${tr}'.axt /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.2bit /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1.2bit '${tr}'.chain'
 
+echo 'chainSort '${tr}'.chain > '${tr}'.sorted.chain'
 
 done
diff --git a/cross_species_comparison/scripts/lastz_commands.sh b/cross_species_comparison/scripts/lastz_commands.sh
new file mode 100644
index 0000000..a382934
--- /dev/null
+++ b/cross_species_comparison/scripts/lastz_commands.sh
@@ -0,0 +1,718 @@
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00001_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00001_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00003_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00003_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00004_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00004_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00005_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00005_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00006_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00006_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00007_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00007_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00008_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00008_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00009_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00009_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00010_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00010_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00011_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00011_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00012_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00012_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00013_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00013_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00014_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00014_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00015_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00015_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00016_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00016_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00017_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00017_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00018_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00018_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00019_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00019_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00020_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00020_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00021_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00021_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00022_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00022_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00023_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00023_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00024_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00024_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00025_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00025_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00026_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00026_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00027_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00027_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00028_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00028_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00029_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00029_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00030_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00030_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00031_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00031_pilon_pilon_mm10.smiCra1.maf
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+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00704_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00704_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00705_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00705_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00706_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00706_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00707_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00707_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00708_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00708_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00709_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00709_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00710_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00710_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00711_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00711_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00712_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00712_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00713_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00713_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00714_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00714_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00715_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00715_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00716_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00716_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00717_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00717_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00718_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00718_pilon_pilon_mm10.smiCra1.maf
+lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/scaffold00719_pilon_pilon.fa H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/scaffold00719_pilon_pilon_mm10.smiCra1.maf
diff --git a/cross_species_comparison/scripts/maf-convert_commands.sh b/cross_species_comparison/scripts/maf-convert_commands.sh
new file mode 100644
index 0000000..cb33564
--- /dev/null
+++ b/cross_species_comparison/scripts/maf-convert_commands.sh
@@ -0,0 +1,718 @@
+maf-convert axt scaffold00001_pilon_pilon_mm10.smiCra1.maf > scaffold00001_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00002_pilon_pilon_mm10.smiCra1.maf > scaffold00002_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00003_pilon_pilon_mm10.smiCra1.maf > scaffold00003_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00004_pilon_pilon_mm10.smiCra1.maf > scaffold00004_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00005_pilon_pilon_mm10.smiCra1.maf > scaffold00005_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00006_pilon_pilon_mm10.smiCra1.maf > scaffold00006_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00007_pilon_pilon_mm10.smiCra1.maf > scaffold00007_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00008_pilon_pilon_mm10.smiCra1.maf > scaffold00008_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00009_pilon_pilon_mm10.smiCra1.maf > scaffold00009_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00010_pilon_pilon_mm10.smiCra1.maf > scaffold00010_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00011_pilon_pilon_mm10.smiCra1.maf > scaffold00011_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00012_pilon_pilon_mm10.smiCra1.maf > scaffold00012_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00013_pilon_pilon_mm10.smiCra1.maf > scaffold00013_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00014_pilon_pilon_mm10.smiCra1.maf > scaffold00014_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00016_pilon_pilon_mm10.smiCra1.maf > scaffold00016_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00017_pilon_pilon_mm10.smiCra1.maf > scaffold00017_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00018_pilon_pilon_mm10.smiCra1.maf > scaffold00018_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00019_pilon_pilon_mm10.smiCra1.maf > scaffold00019_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00020_pilon_pilon_mm10.smiCra1.maf > scaffold00020_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00021_pilon_pilon_mm10.smiCra1.maf > scaffold00021_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00022_pilon_pilon_mm10.smiCra1.maf > scaffold00022_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00023_pilon_pilon_mm10.smiCra1.maf > scaffold00023_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00024_pilon_pilon_mm10.smiCra1.maf > scaffold00024_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00025_pilon_pilon_mm10.smiCra1.maf > scaffold00025_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00026_pilon_pilon_mm10.smiCra1.maf > scaffold00026_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00027_pilon_pilon_mm10.smiCra1.maf > scaffold00027_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00028_pilon_pilon_mm10.smiCra1.maf > scaffold00028_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00029_pilon_pilon_mm10.smiCra1.maf > scaffold00029_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00030_pilon_pilon_mm10.smiCra1.maf > scaffold00030_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00031_pilon_pilon_mm10.smiCra1.maf > scaffold00031_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00032_pilon_pilon_mm10.smiCra1.maf > scaffold00032_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00033_pilon_pilon_mm10.smiCra1.maf > scaffold00033_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00034_pilon_pilon_mm10.smiCra1.maf > scaffold00034_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00035_pilon_pilon_mm10.smiCra1.maf > scaffold00035_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00036_pilon_pilon_mm10.smiCra1.maf > scaffold00036_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00037_pilon_pilon_mm10.smiCra1.maf > scaffold00037_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00038_pilon_pilon_mm10.smiCra1.maf > scaffold00038_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00039_pilon_pilon_mm10.smiCra1.maf > scaffold00039_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00040_pilon_pilon_mm10.smiCra1.maf > scaffold00040_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00041_pilon_pilon_mm10.smiCra1.maf > scaffold00041_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00042_pilon_pilon_mm10.smiCra1.maf > scaffold00042_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00043_pilon_pilon_mm10.smiCra1.maf > scaffold00043_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00044_pilon_pilon_mm10.smiCra1.maf > scaffold00044_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00045_pilon_pilon_mm10.smiCra1.maf > scaffold00045_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00046_pilon_pilon_mm10.smiCra1.maf > scaffold00046_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00047_pilon_pilon_mm10.smiCra1.maf > scaffold00047_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00048_pilon_pilon_mm10.smiCra1.maf > scaffold00048_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00049_pilon_pilon_mm10.smiCra1.maf > scaffold00049_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00050_pilon_pilon_mm10.smiCra1.maf > scaffold00050_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00051_pilon_pilon_mm10.smiCra1.maf > scaffold00051_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00052_pilon_pilon_mm10.smiCra1.maf > scaffold00052_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00053_pilon_pilon_mm10.smiCra1.maf > scaffold00053_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00054_pilon_pilon_mm10.smiCra1.maf > scaffold00054_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00055_pilon_pilon_mm10.smiCra1.maf > scaffold00055_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00056_pilon_pilon_mm10.smiCra1.maf > scaffold00056_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00057_pilon_pilon_mm10.smiCra1.maf > scaffold00057_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00058_pilon_pilon_mm10.smiCra1.maf > scaffold00058_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00059_pilon_pilon_mm10.smiCra1.maf > scaffold00059_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00060_pilon_pilon_mm10.smiCra1.maf > scaffold00060_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00061_pilon_pilon_mm10.smiCra1.maf > scaffold00061_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00062_pilon_pilon_mm10.smiCra1.maf > scaffold00062_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00063_pilon_pilon_mm10.smiCra1.maf > scaffold00063_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00064_pilon_pilon_mm10.smiCra1.maf > scaffold00064_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00065_pilon_pilon_mm10.smiCra1.maf > scaffold00065_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00066_pilon_pilon_mm10.smiCra1.maf > scaffold00066_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00067_pilon_pilon_mm10.smiCra1.maf > scaffold00067_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00068_pilon_pilon_mm10.smiCra1.maf > scaffold00068_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00069_pilon_pilon_mm10.smiCra1.maf > scaffold00069_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00070_pilon_pilon_mm10.smiCra1.maf > scaffold00070_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00071_pilon_pilon_mm10.smiCra1.maf > scaffold00071_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00072_pilon_pilon_mm10.smiCra1.maf > scaffold00072_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00073_pilon_pilon_mm10.smiCra1.maf > scaffold00073_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00074_pilon_pilon_mm10.smiCra1.maf > scaffold00074_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00075_pilon_pilon_mm10.smiCra1.maf > scaffold00075_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00076_pilon_pilon_mm10.smiCra1.maf > scaffold00076_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00077_pilon_pilon_mm10.smiCra1.maf > scaffold00077_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00078_pilon_pilon_mm10.smiCra1.maf > scaffold00078_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00079_pilon_pilon_mm10.smiCra1.maf > scaffold00079_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00080_pilon_pilon_mm10.smiCra1.maf > scaffold00080_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00081_pilon_pilon_mm10.smiCra1.maf > scaffold00081_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00082_pilon_pilon_mm10.smiCra1.maf > scaffold00082_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00083_pilon_pilon_mm10.smiCra1.maf > scaffold00083_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00084_pilon_pilon_mm10.smiCra1.maf > scaffold00084_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00085_pilon_pilon_mm10.smiCra1.maf > scaffold00085_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00086_pilon_pilon_mm10.smiCra1.maf > scaffold00086_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00087_pilon_pilon_mm10.smiCra1.maf > scaffold00087_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00088_pilon_pilon_mm10.smiCra1.maf > scaffold00088_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00089_pilon_pilon_mm10.smiCra1.maf > scaffold00089_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00090_pilon_pilon_mm10.smiCra1.maf > scaffold00090_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00091_pilon_pilon_mm10.smiCra1.maf > scaffold00091_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00092_pilon_pilon_mm10.smiCra1.maf > scaffold00092_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00093_pilon_pilon_mm10.smiCra1.maf > scaffold00093_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00094_pilon_pilon_mm10.smiCra1.maf > scaffold00094_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00095_pilon_pilon_mm10.smiCra1.maf > scaffold00095_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00096_pilon_pilon_mm10.smiCra1.maf > scaffold00096_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00097_pilon_pilon_mm10.smiCra1.maf > scaffold00097_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00098_pilon_pilon_mm10.smiCra1.maf > scaffold00098_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00099_pilon_pilon_mm10.smiCra1.maf > scaffold00099_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00100_pilon_pilon_mm10.smiCra1.maf > scaffold00100_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00101_pilon_pilon_mm10.smiCra1.maf > scaffold00101_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00102_pilon_pilon_mm10.smiCra1.maf > scaffold00102_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00103_pilon_pilon_mm10.smiCra1.maf > scaffold00103_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00104_pilon_pilon_mm10.smiCra1.maf > scaffold00104_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00266_pilon_pilon_mm10.smiCra1.maf > scaffold00266_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00267_pilon_pilon_mm10.smiCra1.maf > scaffold00267_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00268_pilon_pilon_mm10.smiCra1.maf > scaffold00268_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00269_pilon_pilon_mm10.smiCra1.maf > scaffold00269_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00270_pilon_pilon_mm10.smiCra1.maf > scaffold00270_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00271_pilon_pilon_mm10.smiCra1.maf > scaffold00271_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00272_pilon_pilon_mm10.smiCra1.maf > scaffold00272_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00273_pilon_pilon_mm10.smiCra1.maf > scaffold00273_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00274_pilon_pilon_mm10.smiCra1.maf > scaffold00274_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00275_pilon_pilon_mm10.smiCra1.maf > scaffold00275_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00277_pilon_pilon_mm10.smiCra1.maf > scaffold00277_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00278_pilon_pilon_mm10.smiCra1.maf > scaffold00278_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00279_pilon_pilon_mm10.smiCra1.maf > scaffold00279_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00280_pilon_pilon_mm10.smiCra1.maf > scaffold00280_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00292_pilon_pilon_mm10.smiCra1.maf > scaffold00292_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00307_pilon_pilon_mm10.smiCra1.maf > scaffold00307_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00425_pilon_pilon_mm10.smiCra1.maf > scaffold00425_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00426_pilon_pilon_mm10.smiCra1.maf > scaffold00426_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00427_pilon_pilon_mm10.smiCra1.maf > scaffold00427_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00428_pilon_pilon_mm10.smiCra1.maf > scaffold00428_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00429_pilon_pilon_mm10.smiCra1.maf > scaffold00429_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00430_pilon_pilon_mm10.smiCra1.maf > scaffold00430_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00431_pilon_pilon_mm10.smiCra1.maf > scaffold00431_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00432_pilon_pilon_mm10.smiCra1.maf > scaffold00432_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00433_pilon_pilon_mm10.smiCra1.maf > scaffold00433_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00434_pilon_pilon_mm10.smiCra1.maf > scaffold00434_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00435_pilon_pilon_mm10.smiCra1.maf > scaffold00435_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00436_pilon_pilon_mm10.smiCra1.maf > scaffold00436_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00437_pilon_pilon_mm10.smiCra1.maf > scaffold00437_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00438_pilon_pilon_mm10.smiCra1.maf > scaffold00438_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00439_pilon_pilon_mm10.smiCra1.maf > scaffold00439_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00440_pilon_pilon_mm10.smiCra1.maf > scaffold00440_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00441_pilon_pilon_mm10.smiCra1.maf > scaffold00441_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00442_pilon_pilon_mm10.smiCra1.maf > scaffold00442_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00443_pilon_pilon_mm10.smiCra1.maf > scaffold00443_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00444_pilon_pilon_mm10.smiCra1.maf > scaffold00444_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00445_pilon_pilon_mm10.smiCra1.maf > scaffold00445_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00446_pilon_pilon_mm10.smiCra1.maf > scaffold00446_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00447_pilon_pilon_mm10.smiCra1.maf > scaffold00447_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00448_pilon_pilon_mm10.smiCra1.maf > scaffold00448_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00449_pilon_pilon_mm10.smiCra1.maf > scaffold00449_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00450_pilon_pilon_mm10.smiCra1.maf > scaffold00450_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00451_pilon_pilon_mm10.smiCra1.maf > scaffold00451_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00452_pilon_pilon_mm10.smiCra1.maf > scaffold00452_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00453_pilon_pilon_mm10.smiCra1.maf > scaffold00453_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00454_pilon_pilon_mm10.smiCra1.maf > scaffold00454_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00455_pilon_pilon_mm10.smiCra1.maf > scaffold00455_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00456_pilon_pilon_mm10.smiCra1.maf > scaffold00456_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00457_pilon_pilon_mm10.smiCra1.maf > scaffold00457_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00458_pilon_pilon_mm10.smiCra1.maf > scaffold00458_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00459_pilon_pilon_mm10.smiCra1.maf > scaffold00459_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00460_pilon_pilon_mm10.smiCra1.maf > scaffold00460_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00461_pilon_pilon_mm10.smiCra1.maf > scaffold00461_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00462_pilon_pilon_mm10.smiCra1.maf > scaffold00462_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00463_pilon_pilon_mm10.smiCra1.maf > scaffold00463_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00464_pilon_pilon_mm10.smiCra1.maf > scaffold00464_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00465_pilon_pilon_mm10.smiCra1.maf > scaffold00465_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00466_pilon_pilon_mm10.smiCra1.maf > scaffold00466_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00467_pilon_pilon_mm10.smiCra1.maf > scaffold00467_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00468_pilon_pilon_mm10.smiCra1.maf > scaffold00468_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00469_pilon_pilon_mm10.smiCra1.maf > scaffold00469_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00470_pilon_pilon_mm10.smiCra1.maf > scaffold00470_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00471_pilon_pilon_mm10.smiCra1.maf > scaffold00471_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00472_pilon_pilon_mm10.smiCra1.maf > scaffold00472_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00473_pilon_pilon_mm10.smiCra1.maf > scaffold00473_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00474_pilon_pilon_mm10.smiCra1.maf > scaffold00474_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00475_pilon_pilon_mm10.smiCra1.maf > scaffold00475_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00476_pilon_pilon_mm10.smiCra1.maf > scaffold00476_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00477_pilon_pilon_mm10.smiCra1.maf > scaffold00477_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00478_pilon_pilon_mm10.smiCra1.maf > scaffold00478_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00479_pilon_pilon_mm10.smiCra1.maf > scaffold00479_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00480_pilon_pilon_mm10.smiCra1.maf > scaffold00480_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00481_pilon_pilon_mm10.smiCra1.maf > scaffold00481_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00482_pilon_pilon_mm10.smiCra1.maf > scaffold00482_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00483_pilon_pilon_mm10.smiCra1.maf > scaffold00483_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00484_pilon_pilon_mm10.smiCra1.maf > scaffold00484_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00485_pilon_pilon_mm10.smiCra1.maf > scaffold00485_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00486_pilon_pilon_mm10.smiCra1.maf > scaffold00486_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00487_pilon_pilon_mm10.smiCra1.maf > scaffold00487_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00488_pilon_pilon_mm10.smiCra1.maf > scaffold00488_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00489_pilon_pilon_mm10.smiCra1.maf > scaffold00489_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00491_pilon_pilon_mm10.smiCra1.maf > scaffold00491_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00492_pilon_pilon_mm10.smiCra1.maf > scaffold00492_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00493_pilon_pilon_mm10.smiCra1.maf > scaffold00493_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00500_pilon_pilon_mm10.smiCra1.maf > scaffold00500_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00504_pilon_pilon_mm10.smiCra1.maf > scaffold00504_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00505_pilon_pilon_mm10.smiCra1.maf > scaffold00505_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00506_pilon_pilon_mm10.smiCra1.maf > scaffold00506_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00507_pilon_pilon_mm10.smiCra1.maf > scaffold00507_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00508_pilon_pilon_mm10.smiCra1.maf > scaffold00508_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00509_pilon_pilon_mm10.smiCra1.maf > scaffold00509_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00510_pilon_pilon_mm10.smiCra1.maf > scaffold00510_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00513_pilon_pilon_mm10.smiCra1.maf > scaffold00513_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00554_pilon_pilon_mm10.smiCra1.maf > scaffold00554_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00555_pilon_pilon_mm10.smiCra1.maf > scaffold00555_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00557_pilon_pilon_mm10.smiCra1.maf > scaffold00557_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00558_pilon_pilon_mm10.smiCra1.maf > scaffold00558_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00562_pilon_pilon_mm10.smiCra1.maf > scaffold00562_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00563_pilon_pilon_mm10.smiCra1.maf > scaffold00563_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00573_pilon_pilon_mm10.smiCra1.maf > scaffold00573_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00576_pilon_pilon_mm10.smiCra1.maf > scaffold00576_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00578_pilon_pilon_mm10.smiCra1.maf > scaffold00578_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00579_pilon_pilon_mm10.smiCra1.maf > scaffold00579_pilon_pilon_mm10.smiCra1.axt
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+maf-convert axt scaffold00581_pilon_pilon_mm10.smiCra1.maf > scaffold00581_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00582_pilon_pilon_mm10.smiCra1.maf > scaffold00582_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00583_pilon_pilon_mm10.smiCra1.maf > scaffold00583_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00584_pilon_pilon_mm10.smiCra1.maf > scaffold00584_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00585_pilon_pilon_mm10.smiCra1.maf > scaffold00585_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00586_pilon_pilon_mm10.smiCra1.maf > scaffold00586_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00587_pilon_pilon_mm10.smiCra1.maf > scaffold00587_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00588_pilon_pilon_mm10.smiCra1.maf > scaffold00588_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00589_pilon_pilon_mm10.smiCra1.maf > scaffold00589_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00590_pilon_pilon_mm10.smiCra1.maf > scaffold00590_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00591_pilon_pilon_mm10.smiCra1.maf > scaffold00591_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00592_pilon_pilon_mm10.smiCra1.maf > scaffold00592_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00593_pilon_pilon_mm10.smiCra1.maf > scaffold00593_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00594_pilon_pilon_mm10.smiCra1.maf > scaffold00594_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00595_pilon_pilon_mm10.smiCra1.maf > scaffold00595_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00596_pilon_pilon_mm10.smiCra1.maf > scaffold00596_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00597_pilon_pilon_mm10.smiCra1.maf > scaffold00597_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00598_pilon_pilon_mm10.smiCra1.maf > scaffold00598_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00599_pilon_pilon_mm10.smiCra1.maf > scaffold00599_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00600_pilon_pilon_mm10.smiCra1.maf > scaffold00600_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00601_pilon_pilon_mm10.smiCra1.maf > scaffold00601_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00602_pilon_pilon_mm10.smiCra1.maf > scaffold00602_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00603_pilon_pilon_mm10.smiCra1.maf > scaffold00603_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00604_pilon_pilon_mm10.smiCra1.maf > scaffold00604_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00605_pilon_pilon_mm10.smiCra1.maf > scaffold00605_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00606_pilon_pilon_mm10.smiCra1.maf > scaffold00606_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00607_pilon_pilon_mm10.smiCra1.maf > scaffold00607_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00608_pilon_pilon_mm10.smiCra1.maf > scaffold00608_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00609_pilon_pilon_mm10.smiCra1.maf > scaffold00609_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00610_pilon_pilon_mm10.smiCra1.maf > scaffold00610_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00611_pilon_pilon_mm10.smiCra1.maf > scaffold00611_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00612_pilon_pilon_mm10.smiCra1.maf > scaffold00612_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00613_pilon_pilon_mm10.smiCra1.maf > scaffold00613_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00614_pilon_pilon_mm10.smiCra1.maf > scaffold00614_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00615_pilon_pilon_mm10.smiCra1.maf > scaffold00615_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00616_pilon_pilon_mm10.smiCra1.maf > scaffold00616_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00617_pilon_pilon_mm10.smiCra1.maf > scaffold00617_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00618_pilon_pilon_mm10.smiCra1.maf > scaffold00618_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00619_pilon_pilon_mm10.smiCra1.maf > scaffold00619_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00620_pilon_pilon_mm10.smiCra1.maf > scaffold00620_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00621_pilon_pilon_mm10.smiCra1.maf > scaffold00621_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00622_pilon_pilon_mm10.smiCra1.maf > scaffold00622_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00623_pilon_pilon_mm10.smiCra1.maf > scaffold00623_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00624_pilon_pilon_mm10.smiCra1.maf > scaffold00624_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00625_pilon_pilon_mm10.smiCra1.maf > scaffold00625_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00626_pilon_pilon_mm10.smiCra1.maf > scaffold00626_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00627_pilon_pilon_mm10.smiCra1.maf > scaffold00627_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00628_pilon_pilon_mm10.smiCra1.maf > scaffold00628_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00629_pilon_pilon_mm10.smiCra1.maf > scaffold00629_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00630_pilon_pilon_mm10.smiCra1.maf > scaffold00630_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00631_pilon_pilon_mm10.smiCra1.maf > scaffold00631_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00632_pilon_pilon_mm10.smiCra1.maf > scaffold00632_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00633_pilon_pilon_mm10.smiCra1.maf > scaffold00633_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00634_pilon_pilon_mm10.smiCra1.maf > scaffold00634_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00635_pilon_pilon_mm10.smiCra1.maf > scaffold00635_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00636_pilon_pilon_mm10.smiCra1.maf > scaffold00636_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00637_pilon_pilon_mm10.smiCra1.maf > scaffold00637_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00638_pilon_pilon_mm10.smiCra1.maf > scaffold00638_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00639_pilon_pilon_mm10.smiCra1.maf > scaffold00639_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00640_pilon_pilon_mm10.smiCra1.maf > scaffold00640_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00641_pilon_pilon_mm10.smiCra1.maf > scaffold00641_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00642_pilon_pilon_mm10.smiCra1.maf > scaffold00642_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00643_pilon_pilon_mm10.smiCra1.maf > scaffold00643_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00644_pilon_pilon_mm10.smiCra1.maf > scaffold00644_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00645_pilon_pilon_mm10.smiCra1.maf > scaffold00645_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00646_pilon_pilon_mm10.smiCra1.maf > scaffold00646_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00647_pilon_pilon_mm10.smiCra1.maf > scaffold00647_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00648_pilon_pilon_mm10.smiCra1.maf > scaffold00648_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00649_pilon_pilon_mm10.smiCra1.maf > scaffold00649_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00650_pilon_pilon_mm10.smiCra1.maf > scaffold00650_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00651_pilon_pilon_mm10.smiCra1.maf > scaffold00651_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00652_pilon_pilon_mm10.smiCra1.maf > scaffold00652_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00653_pilon_pilon_mm10.smiCra1.maf > scaffold00653_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00654_pilon_pilon_mm10.smiCra1.maf > scaffold00654_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00655_pilon_pilon_mm10.smiCra1.maf > scaffold00655_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00656_pilon_pilon_mm10.smiCra1.maf > scaffold00656_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00657_pilon_pilon_mm10.smiCra1.maf > scaffold00657_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00658_pilon_pilon_mm10.smiCra1.maf > scaffold00658_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00659_pilon_pilon_mm10.smiCra1.maf > scaffold00659_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00660_pilon_pilon_mm10.smiCra1.maf > scaffold00660_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00661_pilon_pilon_mm10.smiCra1.maf > scaffold00661_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00662_pilon_pilon_mm10.smiCra1.maf > scaffold00662_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00663_pilon_pilon_mm10.smiCra1.maf > scaffold00663_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00664_pilon_pilon_mm10.smiCra1.maf > scaffold00664_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00665_pilon_pilon_mm10.smiCra1.maf > scaffold00665_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00666_pilon_pilon_mm10.smiCra1.maf > scaffold00666_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00667_pilon_pilon_mm10.smiCra1.maf > scaffold00667_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00668_pilon_pilon_mm10.smiCra1.maf > scaffold00668_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00669_pilon_pilon_mm10.smiCra1.maf > scaffold00669_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00670_pilon_pilon_mm10.smiCra1.maf > scaffold00670_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00671_pilon_pilon_mm10.smiCra1.maf > scaffold00671_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00672_pilon_pilon_mm10.smiCra1.maf > scaffold00672_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00673_pilon_pilon_mm10.smiCra1.maf > scaffold00673_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00674_pilon_pilon_mm10.smiCra1.maf > scaffold00674_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00675_pilon_pilon_mm10.smiCra1.maf > scaffold00675_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00676_pilon_pilon_mm10.smiCra1.maf > scaffold00676_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00677_pilon_pilon_mm10.smiCra1.maf > scaffold00677_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00678_pilon_pilon_mm10.smiCra1.maf > scaffold00678_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00679_pilon_pilon_mm10.smiCra1.maf > scaffold00679_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00680_pilon_pilon_mm10.smiCra1.maf > scaffold00680_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00681_pilon_pilon_mm10.smiCra1.maf > scaffold00681_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00682_pilon_pilon_mm10.smiCra1.maf > scaffold00682_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00683_pilon_pilon_mm10.smiCra1.maf > scaffold00683_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00684_pilon_pilon_mm10.smiCra1.maf > scaffold00684_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00685_pilon_pilon_mm10.smiCra1.maf > scaffold00685_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00686_pilon_pilon_mm10.smiCra1.maf > scaffold00686_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00687_pilon_pilon_mm10.smiCra1.maf > scaffold00687_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00688_pilon_pilon_mm10.smiCra1.maf > scaffold00688_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00689_pilon_pilon_mm10.smiCra1.maf > scaffold00689_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00690_pilon_pilon_mm10.smiCra1.maf > scaffold00690_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00691_pilon_pilon_mm10.smiCra1.maf > scaffold00691_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00692_pilon_pilon_mm10.smiCra1.maf > scaffold00692_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00693_pilon_pilon_mm10.smiCra1.maf > scaffold00693_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00694_pilon_pilon_mm10.smiCra1.maf > scaffold00694_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00695_pilon_pilon_mm10.smiCra1.maf > scaffold00695_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00696_pilon_pilon_mm10.smiCra1.maf > scaffold00696_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00697_pilon_pilon_mm10.smiCra1.maf > scaffold00697_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00698_pilon_pilon_mm10.smiCra1.maf > scaffold00698_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00699_pilon_pilon_mm10.smiCra1.maf > scaffold00699_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00700_pilon_pilon_mm10.smiCra1.maf > scaffold00700_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00701_pilon_pilon_mm10.smiCra1.maf > scaffold00701_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00702_pilon_pilon_mm10.smiCra1.maf > scaffold00702_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00703_pilon_pilon_mm10.smiCra1.maf > scaffold00703_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00704_pilon_pilon_mm10.smiCra1.maf > scaffold00704_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00705_pilon_pilon_mm10.smiCra1.maf > scaffold00705_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00706_pilon_pilon_mm10.smiCra1.maf > scaffold00706_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00707_pilon_pilon_mm10.smiCra1.maf > scaffold00707_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00708_pilon_pilon_mm10.smiCra1.maf > scaffold00708_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00709_pilon_pilon_mm10.smiCra1.maf > scaffold00709_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00710_pilon_pilon_mm10.smiCra1.maf > scaffold00710_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00711_pilon_pilon_mm10.smiCra1.maf > scaffold00711_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00712_pilon_pilon_mm10.smiCra1.maf > scaffold00712_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00713_pilon_pilon_mm10.smiCra1.maf > scaffold00713_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00714_pilon_pilon_mm10.smiCra1.maf > scaffold00714_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00715_pilon_pilon_mm10.smiCra1.maf > scaffold00715_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00716_pilon_pilon_mm10.smiCra1.maf > scaffold00716_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00717_pilon_pilon_mm10.smiCra1.maf > scaffold00717_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00718_pilon_pilon_mm10.smiCra1.maf > scaffold00718_pilon_pilon_mm10.smiCra1.axt
+maf-convert axt scaffold00719_pilon_pilon_mm10.smiCra1.maf > scaffold00719_pilon_pilon_mm10.smiCra1.axt
diff --git a/cross_species_comparison/scripts/repeatMaskerCommands.sh b/cross_species_comparison/scripts/repeatMaskerCommands.sh
new file mode 100644
index 0000000..90af40b
--- /dev/null
+++ b/cross_species_comparison/scripts/repeatMaskerCommands.sh
@@ -0,0 +1,719 @@
+RepeatMasker -q -xsmall smiCra1/scaffold00001_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00002_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00003_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00004_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00005_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00006_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00007_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00008_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00009_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00010_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00011_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00012_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00013_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00014_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00015_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
+RepeatMasker -q -xsmall smiCra1/scaffold00016_pilon_pilon.fa -default_search_engine hmmer -trf_prgm /home/lecook/.conda/envs/wga/bin/trf -hmmer_dir /home/lecook/.conda/envs/wga/bin/
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diff --git a/mouse/README.md b/mouse/README.md
index e4e5b77..c96c13e 100644
--- a/mouse/README.md
+++ b/mouse/README.md
@@ -243,38 +243,20 @@ therefore if amount that overlaps between each replicate divided by the length o
 
 # Consensus peaks and grouping into putative enhancers and promoters
 
-Separate overlapped replicate peak files:
-```
-less H3K27ac_overlap.narrowPeak| grep "A-3" > H3K27ac_overlap_repA.narrowPeak
-
-less H3K27ac_overlap.narrowPeak| grep "B-3" > H3K27ac_overlap_repB.narrowPeak
-
-less H3K4me3_overlap.narrowPeak| grep "A-2" > H3K4me3_overlap_repA.narrowPeak
-
-less H3K4me3_overlap.narrowPeak| grep "B-2" > H3K4me3_overlap_repB.narrowPeak
-```
-
-Keep only the intersected region:
-```
-bedtools intersect -a H3K27ac_overlap_repA.narrowPeak -b H3K27ac_overlap_repB.narrowPeak > H3K27ac_consensus.narrowPeak
-
-bedtools intersect -a H3K4me3_overlap_repA.narrowPeak -b H3K4me3_overlap_repB.narrowPeak > H3K4me3_consensus.narrowPeak
-```
-
 Find uniquely H3K4me3 sites (i.e. peaks that don't overlap with H3K27ac):
 
 ```
-bedtools intersect -v -a macs2/H3K4me3_consensus.narrowPeak -b macs2/H3K27ac_consensus.narrowPeak > H3K4me3_only.narrowPeak
+bedtools intersect -v -a H3K4me3_overlap.narrowPeak -b H3K27ac_overlap.narrowPeak > H3K4me3_only.narrowPeak
 ```
 
 Find unique H3K27ac sites (i.e. peaks that don't overlap with H3K4me3):
 ```
-bedtools intersect -v macs2/H3K27ac_consensus.narrowPeak -b macs2/H3K4me3_consensus.narrowPeak > H3K27ac_only.narrowPeak
+bedtools intersect -v -a H3K27ac_overlap.narrowPeak -b H3K4me3_overlap.narrowPeak > H3K27ac_only.narrowPeak
 ```
 
 Find peaks common between H3K27ac & H3K4me3 with a reciprocal overlap of at least 50%.
 ```
-bedtools intersect -f 0.5 -r -a macs2/H3K4me3_consensus.narrowPeak -b macs2/H3K27ac_consensus.narrowPeak > H3K4me3_and_H3K27ac.narrowPeak
+bedtools intersect -f 0.5 -r -a H3K4me3_only.narrowPeak -b H3K27ac_only.narrowPeak > H3K4me3_and_H3K27ac.narrowPeak
 ```
 
 
-- 
GitLab