From c16c4b680e1744e18b60a86b9fc070d242befbaa Mon Sep 17 00:00:00 2001
From: Laura Cook <l.cook2@student.unimelb.edu.au>
Date: Fri, 7 Aug 2020 20:17:55 +1000
Subject: [PATCH] updated config files
---
dunnart/configs/.multiqc_config.yaml | 124 ++++++++++++++++++++-------
dunnart/configs/SRR.txt | 10 +--
2 files changed, 97 insertions(+), 37 deletions(-)
diff --git a/dunnart/configs/.multiqc_config.yaml b/dunnart/configs/.multiqc_config.yaml
index d6ec761..2a5e8c7 100644
--- a/dunnart/configs/.multiqc_config.yaml
+++ b/dunnart/configs/.multiqc_config.yaml
@@ -2,6 +2,15 @@ title: "Histone ChIP-seq QC for dunnart craniofacial tissue: H3K4me3 & H3K27ac"
intro_text: ""
report_comment: "Generated on DATE"
+run_modules:
+ - custom_content
+ - fastqc
+ - samtools
+ - picard
+ - preseq
+ - deeptools
+ - phantompeakqualtools
+
report_header_info:
- Contact E-mail: 'lecook@student.unimelb.edu.au'
@@ -10,12 +19,12 @@ report_header_info:
module_order:
- MACS2
- MACS2_narrowPeak_count
- - deepTools
- - Preseq:
+ - deeptools
+ - preseq:
genome_size: 3074798085
read_length: 150
- - Samtools
- - Picard
+ - samtools
+ - picard
- phantompeakqualtools
- bowtie2:
name: 'Bowtie2'
@@ -24,33 +33,84 @@ module_order:
log_filesize_limit: 5000000000
-custom_data:
- encode_metrics:
- plot_type: 'generalstats'
- file_format: 'tsv'
- pconfig:
- - NRF:
- namespace: "NRF"
- title: "NRF"
- description: "ratio between the number of positions in the genome that uniquely mapped reads map to and the total number of uniquely mappable reads"
- max: 1
- min: 0
- scale: 'RdYlGn'
- - PBC1:
- namespace: "PBC1"
- title: "PBC1"
- description: "ratio of genomic locations with EXACTLY one read pair over the genomic locations with AT LEAST one read pair"
- max: 1
- min: 0
- scale: 'RdYlGn'
- - PBC2:
- namespace: "PBC2"
- title: "PBC2"
- description: "ratio of genomic locations with EXACTLY one read pair over the genomic locations with EXACTLY two read pairs"
- max: 10
- min: 0
- scale: 'RdYlGn'
+id: 'frip_score'
+section_name: 'MACS2 FRiP score'
+plot_type: 'bargraph'
+anchor: 'frip_score'
+pconfig:
+ title: 'FRiP score'
+ ylab: 'FRiP score'
+ ymax: 1
+ ymin: 0
+ tt_decimals: 2
+
+id: 'peak_count'
+section_name: 'MACS2 peak count'
+description: "is calculated from total number of peaks called by
+ <a href='https://github.com/taoliu/MACS' target='_blank'>MACS2</a>"
+plot_type: 'bargraph'
+anchor: 'peak_count'
+pconfig:
+ title: 'Total peak count'
+ ylab: 'Peak count'
+
+id: 'strand_shift_correlation'
+section_name: 'spp strand-shift correlation'
+description: "generated using run_spp.R script from
+ <a href='https://github.com/kundajelab/phantompeakqualtools' target='_blank'>phantompeakqualtools</a>."
+plot_type: 'linegraph'
+anchor: 'strand_shift_correlation'
+pconfig:
+ title: 'Strand-shift correlation plot'
+ ylab: 'Cross-correlation'
+ xlab: 'Strand-shift (bp)'
+ xDecimals: False
+ tt_label: 'Strand-shift (bp) {point.x}: {point.y:.2f} Cross-correlation'
+
+id: 'nsc_coefficient'
+section_name: 'spp NSC coefficient'
+description: "generated using run_spp.R script from
+ <a href='https://github.com/kundajelab/phantompeakqualtools' target='_blank'>phantompeakqualtools</a>."
+plot_type: 'bargraph'
+anchor: 'nsc_coefficient'
+pconfig:
+ title: 'Normalized strand cross-correlation coefficient'
+ ylab: 'NSC coefficient'
+ ymin: 1
+ tt_decimals: 1
+
+id: 'rsc_coefficient'
+section_name: 'spp RSC coefficient'
+description: "generated using run_spp.R script from
+ <a href='https://github.com/kundajelab/phantompeakqualtools' target='_blank'>phantompeakqualtools</a>."
+plot_type: 'bargraph'
+anchor: 'rsc_coefficient'
+pconfig:
+ title: 'Relative strand cross-correlation coefficient'
+ ylab: 'RSC coefficient'
+ ymin: 0
+ tt_decimals: 1
+
+
+report_section_order:
+ frip_score:
+ before: peak_count
+ strand_shift_correlation:
+ before: peak_annotation
+ nsc_coefficient:
+ before: strand_shift_correlation
+ rsc_coefficient:
+ before: nsc_coefficient
+
+custom_plot_config:
+ picard_insert_size:
+ cpswitch_c_active: False
+ smooth_points: 1000
sp:
- encode_metrics:
- fn: '*encodeQC.txt'
+ preseq:
+ fn: '*.ccurve.txt'
+ deeptools/plotFingerprintOutRawCounts:
+ fn: '*plotFingerprint*'
+ deeptools/plotProfile:
+ fn: '*plotProfile*'
diff --git a/dunnart/configs/SRR.txt b/dunnart/configs/SRR.txt
index ed29c6a..0e334a7 100644
--- a/dunnart/configs/SRR.txt
+++ b/dunnart/configs/SRR.txt
@@ -1,5 +1,5 @@
-IP Input
-A-2_H3K4me3 A-1_input
-A-3_H3K27ac A-1_input
-B-2_H3K4me3 B-1_input
-B-3_H3K27ac B-1_input
+IP Input mark
+A-2_H3K4me3 A-1_input H3K4me3
+A-3_H3K27ac A-1_input H3K27ac
+B-2_H3K4me3 B-1_input H3K4me3
+B-3_H3K27ac B-1_input H3K27ac
--
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