<?xml version="1.0"?>
<?xml-stylesheet type="text/css" href="http://deep.mpi-inf.mpg.de/DAC/files/style/deep_process_style.css"?>
<process>
<name>CHP</name>
<version>1</version>
<author>
<name>Andreas Richter, Peter Ebert</name>
<email>arichter@ie-freiburg.mpg.de, pebert@mpi-inf.mpg.de</email>
</author>
<description>
Process CHPv1 has been used to analyse the first set of DEEP pilot data.
* {genomesize}: effective genome size (for deepTools and MACS2): for deeply sequenced samples and random mapping strategy approximated by (genome size) - (#N)
* human hs37d5 (1k genomes): 2.9e9
* mouse mm10: 2.65e9
* {fragment_length}: individual median fragment length/insert size of each sample derived from the BAM file (based on alignment statistics from HD [see email from Barbara Hutter, 16 October 2013] or computed by PE_fragment_size)
* use most recent deeptools version from github and most recent MACS2 version
</description>
<inputs>
<filetype>
<identifier>ALNvX_histone.bam</identifier>
<format></format>
<quantity>collection</quantity>
<comment></comment>
</filetype>
<filetype>
<identifier>ALNvX_input.bam</identifier>
<format></format>
<quantity>single</quantity>
<comment></comment>
</filetype>
<filetype>
<identifier>ALNvX.bai</identifier>
<format></format>
<quantity>collection</quantity>
<comment>Index files are renamed internally to .bam.bai since deepTools is expecting index naming like this</comment>
</filetype>
</inputs>
<references>
<filetype>
<identifier>filtered_regions</identifier>
<format>BED</format>
<quantity>single</quantity>
<comment>ENCODE blacklist extended by A. Richter (FB); see DCC/download/results/references/annotations</comment>
</filetype>
<filetype>
<identifier>reference_genome</identifier>
<format>2bit</format>
<quantity>single</quantity>
<comment>The reference genome file; see DCC/download/results/references/genomes</comment>
</filetype>
<filetype>
<identifier>plot_regions</identifier>
<format>BED</format>
<quantity>single</quantity>
<comment>Control regions obtained from A. Richter (FB) for quality control of ChIPseq samples; see DCC/download/results/references/annotations</comment>
</filetype>
</references>
<outputs>
<filetype>
<identifier>samplesID.PROCESS.DATE.corplot.cormethod</identifier>
<format>deepTools graphics PNG</format>
<quantity>single</quantity>
<comment></comment>
</filetype>
<filetype>
<identifier>samplesID.PROCESS.DATE.fgprplot</identifier>
<format>deepTools graphics PNG</format>
<quantity>single</quantity>
<comment></comment>
</filetype>
<filetype>
<identifier>sampleID.PROCESS.DATE.gcbplot</identifier>
<format>deepTools graphics PNG</format>
<quantity>collection</quantity>
<comment></comment>
</filetype>
<filetype>
<identifier>sampleID.PROCESS.DATE.gcbfreq</identifier>
<format>tab-separated text file</format>
<quantity>collection</quantity>
<comment></comment>
</filetype>
<filetype>
<identifier>sampleIDs.PROCESS.DATE.bamcomp.scalemethod</identifier>
<format>bigwig</format>
<quantity>collection</quantity>
<comment>Always compare a signal vs the input</comment>
</filetype>
<filetype>
<identifier>sampleID.PROCESS.DATE.bamcov.seqDepthNorm</identifier>
<format>bigwig</format>
<quantity>collection</quantity>
<comment></comment>
</filetype>
<filetype>
<identifier>sampleID.PROCESS.DATE.ctrlreg</identifier>
<format>graphics PNG</format>
<quantity>collection</quantity>
<comment></comment>
</filetype>
</outputs>
<software>
<tool>
<name>region_filter.py</name>
<version>0.1</version>
<command_line><![CDATA[ region_filter.py --bamfile {ALNvX_*.bam} --regions {filtered_regions} --output BAM_filtered.tmp ]]></command_line>
<loop></loop>
<comment>Script to generate a temporary BAM file with ENCODE blacklist regions excluded, only relevant for bamCorrelate tool. The filtered BAM file is discarded at the end of this process</comment>
</tool>
<tool>
<name>bamCorrelate (deepTools)</name>
<version>1.5.7-5-gcbab7b3</version>
<command_line><![CDATA[ bamCorrelate bins -p {numproc} --bamfiles BAMs_filtered.tmp --plotFile {samplesID.PROCESS.DATE.corplot.cormethod} --corMethod pearson --labels {labels} --binSize 1000 --numberOfSamples 1000000 --fragmentLength {all_median_fraglen} ]]></command_line>
<loop></loop>
<comment>Window/bin size of 1kb since multiple narrow signals will be merged with default value (10kb), 1m samples</comment>
</tool>
<tool>
<name>bamFingerprint (deepTools)</name>
<version>1.5.7-5-gcbab7b3</version>
<command_line><![CDATA[ bamFingerprint -p {numproc} --bamfiles {ALNvX_*.bam} --plotFile {samplesID.PROCESS.DATE.fgpplot} --labels {labels} --fragmentLength {all_median_fraglen} --numberOfSamples 500000 ]]></command_line>
<loop></loop>
<comment></comment>
</tool>
<tool>
<name>computeGCBias (deepTools)</name>
<version>1.5.7-5-gcbab7b3</version>
<command_line><![CDATA[ computeGCBias -p {numproc} --bamfile {ALNvX_*.bam} --effectiveGenomeSize {genomesize} --genome {reference_genome} --fragmentLength {_median_fraglen} --sampleSize 50000000 --GCbiasFrequenciesFile {sampleID.PROCESS.DATE.gcbfreq} --biasPlot {sampleID.PROCESS.DATE.gcbplot} ]]></command_line>
<loop></loop>
<comment></comment>
</tool>
<tool>
<name>MACS2</name>
<version>2.0.10.20131216 (tag:beta)</version>
<command_line><![CDATA[ macs2 callpeak -t {ALNvX_histone.bam} -c {ALNvX_input.bam} -f BAM --gsize {genomesize} --keep-dup all --name {_name_prefix} --nomodel --extsize {_median_fraglen} --qvalue 0.05 {broad} ]]></command_line>
<loop></loop>
<comment>parameter "--broad" for samples H3K4me1/H3K27me3/H3K36me/H3K9me3; default q-value cutoff of 0.05 is recommended by the author at least for broad marks and approved by A. Richter for all marks</comment>
</tool>
<tool>
<name>bamCompare (deepTools)</name>
<version>1.5.7-5-gcbab7b3</version>
<command_line><![CDATA[ bamCompare -p {numproc} --bamfile1 {ALNvX_histone.bam} --bamfile2 {ALNvX_input.bam} --outFileName {sampleIDs.PROCESS.DATE.bamcomp.scalemethod} --outFileFormat bigwig --scaleFactorsMethod {_scaling_method} --ratio log2 --fragmentLength {_median_fraglen} ]]></command_line>
<loop></loop>
<comment>scaling_method: "readCount" for samples H3K27me3/H3K9me3, "SES" else</comment>
</tool>
<tool>
<name>bamCoverage (deepTools)</name>
<version>1.5.7-5-gcbab7b3</version>
<command_line><![CDATA[ bamCoverage -p {numproc} --bam {bamfile} --outFileName {sampleID.PROCESS.DATE.bamcov.seqDepthNorm} --outFileFormat bigwig --normalizeTo1x {genomesize} --fragmentLength {_median_fraglen} ]]></command_line>
<loop></loop>
<comment>report read coverage normalized to 1x sequencing depth</comment>
</tool>
<tool>
<name>signal_plotter.py</name>
<version>0.1</version>
<command_line><![CDATA[ signal_plotter.py --signal {sampleID_histone.PROCESS.DATE.bamcov.seqDepthNorm} --input {sampleID_input.PROCESS.DATE.bamcov.seqDepthNorm} --regions {plot_regions} --outfile {sampleID.PROCESS.DATE.ctrlreg} ]]></command_line>
<loop></loop>
<comment></comment>
</tool>
</software>
</process>