Mercurial > repos > kyost > atac_primer_tool

comparison filter_bam.bash @ 5:3cd53127a838 draft default tip

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planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
author kyost
date Fri, 04 May 2018 02:24:47 -0400
parents fd3ea97a96bc
children
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4:72571a30f17b 5:3cd53127a838
27 echo $name > name 27 echo $name > name
28 paste name count > $read_counts 28 paste name count > $read_counts
29 29
30 #create bed file of fragments for each bam file 30 #create bed file of fragments for each bam file
31 31
32 samtools view -b -L $ext_peak_file $bam_file > $filtered_bam_file 32 samtools view -b -F 4 -L $ext_peak_file $bam_file > $filtered_bam_file
33 33
34 rm name 34 rm name
35 rm count 35 rm count