formatting

dunnart/README.md

-# chipseq-pipeline #
+# chipseq-pipeline
 
 ChIP-seq for H3K4me3 and H3K27ac for craniofacial tissue collection from day of birth dunnart (_Sminthopsis crassicaudata_) pouch young.
 
@@ -295,8 +295,8 @@ bowtie2-build /data/projects/punim0586/lecook/chip/reference_data/bowtie2/dunnar
 
 Uses samtools and picards MarkDuplicates to remove low quality reads. This is based on and in accordance with the ENCODE Guidelines and pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2)
 
-`-q 30`: remove reads with MAPQ score below 30
-`-f 2`: keep proper pairs
+- `-q 30`: remove reads with MAPQ score below 30
+- `-f 2`: keep proper pairs
 
 ### rule markDups:
 
@@ -438,8 +438,8 @@ Align trimmed read 1 (not paired) with bowtie2 and use it for filtering step (no
 
 Uses samtools and picards MarkDuplicates to remove low quality reads. This is based on and in accordance with the ENCODE Guidelines and pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2)
 
-`-q 30`: remove reads with MAPQ score below 30
-`-f 2`: keep proper pairs
+- `-q 30`: remove reads with MAPQ score below 30
+- `-f 2`: keep proper pairs
 
 ### rule bamtobed_crossC:
 
@@ -549,7 +549,7 @@ Overlap replicate peaks for H3K4me3.
 
 Overlap replicate peaks for H3K27ac.
 
-# Consensus peaks and grouping into putative enhancers and promoters
+# 10. Consensus peaks and grouping into putative enhancers and promoters
 
 Separate overlapped replicate peak files:
 ```
@@ -585,7 +585,7 @@ Find peaks common between H3K27ac & H3K4me3 with a reciprocal overlap of at leas
 bedtools intersect -f 0.5 -r -a macs2/H3K4me3_consensus.narrowPeak -b macs2/H3K27ac_consensus.narrowPeak > H3K4me3_and_H3K27ac.narrowPeak
 ```
 
-# Find overlap with TWARs
+# 11. Find overlap with TWARs
 
 ## Get dunnart bed coordinates for TWARs