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Commit c16c4b68 authored by Laura Cook's avatar Laura Cook
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updated config files

parent 77cc4eff
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...@@ -2,6 +2,15 @@ title: "Histone ChIP-seq QC for dunnart craniofacial tissue: H3K4me3 & H3K27ac" ...@@ -2,6 +2,15 @@ title: "Histone ChIP-seq QC for dunnart craniofacial tissue: H3K4me3 & H3K27ac"
intro_text: "" intro_text: ""
report_comment: "Generated on DATE" report_comment: "Generated on DATE"
run_modules:
- custom_content
- fastqc
- samtools
- picard
- preseq
- deeptools
- phantompeakqualtools
report_header_info: report_header_info:
- Contact E-mail: 'lecook@student.unimelb.edu.au' - Contact E-mail: 'lecook@student.unimelb.edu.au'
...@@ -10,12 +19,12 @@ report_header_info: ...@@ -10,12 +19,12 @@ report_header_info:
module_order: module_order:
- MACS2 - MACS2
- MACS2_narrowPeak_count - MACS2_narrowPeak_count
- deepTools - deeptools
- Preseq: - preseq:
genome_size: 3074798085 genome_size: 3074798085
read_length: 150 read_length: 150
- Samtools - samtools
- Picard - picard
- phantompeakqualtools - phantompeakqualtools
- bowtie2: - bowtie2:
name: 'Bowtie2' name: 'Bowtie2'
...@@ -24,33 +33,84 @@ module_order: ...@@ -24,33 +33,84 @@ module_order:
log_filesize_limit: 5000000000 log_filesize_limit: 5000000000
custom_data: id: 'frip_score'
encode_metrics: section_name: 'MACS2 FRiP score'
plot_type: 'generalstats' plot_type: 'bargraph'
file_format: 'tsv' anchor: 'frip_score'
pconfig: pconfig:
- NRF: title: 'FRiP score'
namespace: "NRF" ylab: 'FRiP score'
title: "NRF" ymax: 1
description: "ratio between the number of positions in the genome that uniquely mapped reads map to and the total number of uniquely mappable reads" ymin: 0
max: 1 tt_decimals: 2
min: 0
scale: 'RdYlGn' id: 'peak_count'
- PBC1: section_name: 'MACS2 peak count'
namespace: "PBC1" description: "is calculated from total number of peaks called by
title: "PBC1" <a href='https://github.com/taoliu/MACS' target='_blank'>MACS2</a>"
description: "ratio of genomic locations with EXACTLY one read pair over the genomic locations with AT LEAST one read pair" plot_type: 'bargraph'
max: 1 anchor: 'peak_count'
min: 0 pconfig:
scale: 'RdYlGn' title: 'Total peak count'
- PBC2: ylab: 'Peak count'
namespace: "PBC2"
title: "PBC2" id: 'strand_shift_correlation'
description: "ratio of genomic locations with EXACTLY one read pair over the genomic locations with EXACTLY two read pairs" section_name: 'spp strand-shift correlation'
max: 10 description: "generated using run_spp.R script from
min: 0 <a href='https://github.com/kundajelab/phantompeakqualtools' target='_blank'>phantompeakqualtools</a>."
scale: 'RdYlGn' 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: sp:
encode_metrics: preseq:
fn: '*encodeQC.txt' fn: '*.ccurve.txt'
deeptools/plotFingerprintOutRawCounts:
fn: '*plotFingerprint*'
deeptools/plotProfile:
fn: '*plotProfile*'
IP Input IP Input mark
A-2_H3K4me3 A-1_input A-2_H3K4me3 A-1_input H3K4me3
A-3_H3K27ac A-1_input A-3_H3K27ac A-1_input H3K27ac
B-2_H3K4me3 B-1_input B-2_H3K4me3 B-1_input H3K4me3
B-3_H3K27ac B-1_input B-3_H3K27ac B-1_input H3K27ac
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