Mercurial > repos > kyost > atac_primer_tool
comparison filter_bam.bash @ 5:3cd53127a838 draft default tip
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
author | kyost |
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date | Fri, 04 May 2018 02:24:47 -0400 |
parents | fd3ea97a96bc |
children |
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4:72571a30f17b | 5:3cd53127a838 |
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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 |