Mercurial > repos > kyost > atac_primer_tool
view filter_bam.bash @ 3:fbfe7b785ea7 draft
Add test for 0 standard deviation.
author | kyost |
---|---|
date | Wed, 02 May 2018 13:20:01 -0400 |
parents | fd3ea97a96bc |
children | 3cd53127a838 |
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#Requires bam files and bed file containing coordinates of peaks of interest #Generates filtered bams and library size file to upload into Galaxy #required arguements: #($1): bam file #($2): bed file containing regions of interest #Usage: filter_bam /pathtofolder/ qPCR_peaks.bed #outputs: #Filtered bam files containing reads in regions of interest #read_counts: txt file containing number of mapped reads in each bam file, used for normalization bam_file=$1 peak_file=$2 chrom_sizes=$3 ext_peak_file=$4 filtered_bam_file=$5 read_counts=$6 name=$7 bedtools slop -i $peak_file -g $chrom_sizes -b 2000 | sort -k1,1 -k2,2n - > $ext_peak_file samtools index $bam_file samtools view -c -F 1284 $bam_file > count echo $name > name paste name count > $read_counts #create bed file of fragments for each bam file samtools view -b -L $ext_peak_file $bam_file > $filtered_bam_file rm name rm count