From d50d6b99fca5402335bc4722cfa1741bd08509f9 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <Venkat.Malladi@utsouthwestern.edu>
Date: Tue, 16 Aug 2016 14:09:56 -0500
Subject: [PATCH] Call peaks for H3K4me3.
---
call-peaks-macs-single.sh | 169 ++++++++++++++++++++++++++++++++++++++
1 file changed, 169 insertions(+)
create mode 100644 call-peaks-macs-single.sh
diff --git a/call-peaks-macs-single.sh b/call-peaks-macs-single.sh
new file mode 100644
index 0000000..6e78c91
--- /dev/null
+++ b/call-peaks-macs-single.sh
@@ -0,0 +1,169 @@
+#!/bin/bash
+# call-peaks-macs.sh
+
+script_name="call-peaks-macs2.sh"
+script_ver="2.1.0"
+
+#Help function
+usage() {
+ echo "-h --Help documentation for $script_name"
+ echo "-f --File path to experiment tagAlign files."
+ echo "-s --File path to control tagAlign files."
+ echo "-x --File path to experiment cross-correlation scores."
+ echo "-r --UCSC Reference genome (e.g. hg19, mm10)"
+ echo "-o --Path to output directory"
+ echo "-v --Version of script"
+ echo "Example: $script_name -f 'foo1.tagAlign.gz' -s 'con1.tagAlign.gz' -x 'foo1.cc' -r 'hg19' [-o '/path/to/output/dir/']"
+ exit 1
+}
+
+# Version function
+version(){
+ echo "$script_name $script_ver"
+ exit 1
+}
+
+
+# Peak calling function
+call_peak() {
+ # Establish variables
+
+ experiment=$1
+ control=$2
+ xcor_scores_input=$3
+ chrom_sizes=$4
+ genomesize=$5
+ out_dir=$6
+
+ #Extract the fragment length estimate from cross-correlation scores file
+ fraglen=`cat $xcor_scores_input | grep "predicted" | cut -f6 -d ' '`
+ echo $fraglen
+
+ # Generate narrow peaks and preliminary signal tracks
+ base_fn=$(basename "${experiment}")
+ prefix=${base_fn%.tagAlign.gz}
+ macs2 callpeak -t $experiment -c $control -f BED -n $out_dir/$prefix -g $genomesize -p 1e-5 --nomodel --shift 0 --extsize $fraglen --keep-dup all -B --SPMR
+
+ # Generate fold enrichment signal tracks
+ macs2 bdgcmp -t $out_dir/$prefix\_treat_pileup.bdg -c $out_dir/$prefix\_control_lambda.bdg --outdir $out_dir -o $prefix\_FE.bdg -m FE
+
+ # Genearte bigWigs from bedgraph to support vizualization
+ bedtools slop -i $out_dir/$prefix\_FE.bdg -g /$chrom_sizes -b 0 | bedClip stdin $chrom_sizes $out_dir/$prefix.fc.signal.bedgraph
+ bedSort $out_dir/$prefix.fc.signal.bedgraph $out_dir/$prefix.sorted.fc.signal.bedgraph
+ bedGraphToBigWig $out_dir/$prefix.sorted.fc.signal.bedgraph $chrom_sizes $out_dir/$prefix.fc_signal.bw
+ rm $out_dir/$prefix.fc.signal.bedgraph
+ rm $out_dir/$prefix.sorted.fc.signal.bedgraph
+
+ # Generate fold enrichment signal tracks
+
+ # Compute sval = min(no. of reads in ChIP, no. of reads in control) / 1,000,000
+ experiment_reads=`gzip -dc $experiment | wc -l | cut -f1`
+ control_reads=`gzip -dc $control | wc -l | cut -f1`
+ if [ $experiment_reads -ge $control_reads ]; then
+ min=$control_reads
+ else
+ min=$experiment_reads
+ fi
+ sval=`echo $min/1000000 | bc -l`
+
+ macs2 bdgcmp -t $out_dir/$prefix\_treat_pileup.bdg -c $out_dir/$prefix\_control_lambda.bdg --outdir $out_dir -o $prefix\_ppois.bdg -m ppois -S $sval
+
+ # Genearte bigWigs from bedgraph to support vizualization
+ bedtools slop -i $out_dir/$prefix\_ppois.bdg -g $chrom_sizes -b 0 | bedClip stdin $chrom_sizes $out_dir/$prefix.pval.signal.bedgraph
+ bedSort $out_dir/$prefix.pval.signal.bedgraph $out_dir/$prefix.sorted.pval.signal.bedgraph
+ bedGraphToBigWig $out_dir/$prefix.sorted.pval.signal.bedgraph $chrom_sizes $out_dir/$prefix.pval_signal.bw
+ rm $out_dir/$prefix.pval.signal.bedgraph
+ rm $out_dir/$prefix.sorted.pval.signal.bedgraph
+}
+
+main(){
+
+ # Load required modules
+ module load python/2.7.x-anaconda
+ module load R/3.1.0-intel
+ module load macs/2.1.0-20151222
+ module load gcc/4.8.1
+ module load bedtools/2.17.0
+ module load UCSC_userApps/v317
+
+ # Parsing options
+ OPTIND=1 # Reset OPTIND
+ while getopts :f:s:x:r:o:hv opt
+ do
+ case $opt in
+ f) aln=$OPTARG;;
+ s) control=$OPTARG;;
+ x) aln_cross=$OPTARG;;
+ r) ucsc_reference=$OPTARG;;
+ o) out=$OPTARG;;
+ h) usage;;
+ v) version;;
+ esac
+ done
+
+ shift $(($OPTIND -1))
+
+ # Check for mandatory options
+ if [[ -z $aln ]] || [[ -z $control ]] || [[ -z $ucsc_reference ]] || [[ -z $aln_cross ]]; then
+ usage
+ fi
+
+ # Check if length of arguments in aln1, aln2 and exp are the same
+ array_aln=(${aln//[,| ]/ })
+ array_control=(${control//[,| ]/ })
+ array_aln_cross=(${aln_cross//[,| ]/ })
+ # Define the genome size to use
+ if [ $ucsc_reference = 'hg19' ]; then
+ genome_size='hs'
+ elif [ $ucsc_reference = 'mm10' ]; then
+ genome_size='mm'
+ elif [ $ucsc_reference = 'mm9' ]; then
+ genome_size='mm'
+ else
+ usage
+ fi
+
+ # Define the output directory, if none defined make the location relative to first file
+ if [ -z $out ]; then
+ one_parent=$(dirname "${aln}")
+ out_dir=$(dirname "${one_parent}")\/$script_name-$script_ver/
+ else
+ out_dir=$out\/$script_name-$script_ver
+ fi
+
+ if [ ! -d $out_dir ]; then
+ mkdir $out_dir
+ fi
+
+ # Align if file doesn't exist
+ if [ ! -e $out_dir/metadata.json ]; then
+
+ # split files
+ rep1=${aln}
+ con1=${control}
+ rep1_xcor=${aln_cross}
+
+ echo "* Downloading chrom.sizes..."
+ fetchChromSizes $ucsc_reference > $out_dir/chrom.sizes
+ chrom_sizes=$out_dir/chrom.sizes
+
+ # Call peaks Replicates 1 and 2
+ call_peak $rep1 $con1 $rep1_xcor $chrom_sizes $genome_size $out_dir
+
+ # Remove chrom sizes
+ rm $out_dir/chrom.sizes
+
+ # Get input and output files and then print out metadata.json file
+ input_files=("${array_aln[@]}" "${array_control[@]}" "${array_aln_cross[@]}" "$ucsc_reference")
+ printf -v input "\"%s\"," "${input_files[@]}"
+ input=${input%,}
+ output_file=($out_dir\/*)
+ printf -v output "\"%s\"," "${output_file[@]}"
+ output=${output%,}
+ printf '{"script name":"%s","script version":"%s", "input files": [%s], "output files": [%s]}' "$script_name" "$script_ver" "$input" "$output" | python -m json.tool > $out_dir/metadata.json
+ else
+ echo "* Peaks have been called"
+ fi
+}
+
+main "$@"
--
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