Mercurial > repos > kyost > atac_primer_tool
annotate filter_bam.bash @ 0:fd3ea97a96bc draft
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
author | kyost |
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date | Sat, 28 Apr 2018 15:07:26 -0400 |
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children | 3cd53127a838 |
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planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
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1 #Requires bam files and bed file containing coordinates of peaks of interest |
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planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
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2 #Generates filtered bams and library size file to upload into Galaxy |
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3 |
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4 #required arguements: |
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5 #($1): bam file |
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planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
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6 #($2): bed file containing regions of interest |
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planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
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7 |
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planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
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8 #Usage: filter_bam /pathtofolder/ qPCR_peaks.bed |
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9 |
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planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
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10 #outputs: |
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11 #Filtered bam files containing reads in regions of interest |
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planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
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12 #read_counts: txt file containing number of mapped reads in each bam file, used for normalization |
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13 |
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14 bam_file=$1 |
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planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
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15 peak_file=$2 |
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16 chrom_sizes=$3 |
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17 ext_peak_file=$4 |
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planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
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18 filtered_bam_file=$5 |
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planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
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19 read_counts=$6 |
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20 name=$7 |
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21 |
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22 bedtools slop -i $peak_file -g $chrom_sizes -b 2000 | sort -k1,1 -k2,2n - > $ext_peak_file |
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23 |
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24 samtools index $bam_file |
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25 |
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26 samtools view -c -F 1284 $bam_file > count |
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27 echo $name > name |
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28 paste name count > $read_counts |
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29 |
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30 #create bed file of fragments for each bam file |
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31 |
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32 samtools view -b -L $ext_peak_file $bam_file > $filtered_bam_file |
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33 |
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34 rm name |
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35 rm count |