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May 15, 2021 22:08
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Count all reads, nucleosomal-free reads and mononucleosomal reads in a bam file.
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#!/bin/bash | |
#$ -N samtools.count | |
#$ -cwd | |
#$ -q long-sl7,mem_512_12h,mem_512 | |
#$ -l virtual_free=50G,h_rt=12:00:00,disk=50G | |
#$ -M anamaria.elek@crg.eu | |
#$ -o samtools.count.out | |
#$ -pe smp 16 | |
#$ -j y | |
SAMTOOLS_PATH="/users/asebe/aelek/bin/samtools-1.12" | |
echo $(date) | |
samtools_count () { | |
local BAM=$1 | |
local COUNTS=${BAM%%bam}counts.txt | |
local OUT=${BAM%%bam}counts.tmp | |
local ROWS=$( dirname $BAM )/tmp.txt | |
printf "FILE\nREADS\nNFR\nMONO\nOTHER" > $ROWS | |
echo $(date): Counting reads in $BAM | |
READS=$( ${SAMTOOLS_PATH}/samtools view -c $BAM ) | |
NFR=$( ${SAMTOOLS_PATH}/samtools view $BAM | awk -v LEN=147 '{if ( $9 <= LEN && $9 >= -(LEN) && $9 != 0) print $0}' | wc -l ) | |
MONO=$( ${SAMTOOLS_PATH}/samtools view $BAM | awk -v LENMIN=147 -v LENMAX=240 '{if ( $9 > LENMIN && $9 < LENMAX || $9 < -(LENMIN) && $9 > -(LENMAX) ) print $0}' | wc -l ) | |
OTHER=$( ${SAMTOOLS_PATH}/samtools view $BAM | awk -v LEN=240 '{if ( $9 >= LEN || $9 <= -(LEN) || $9 == 0) print $0}' | wc -l ) | |
printf "$BAM\n$READS\n$NFR\n$MONO\n$OTHER" > $OUT | |
paste $ROWS $OUT > $COUNTS | |
rm $OUT # $ROWS | |
echo $(date): Done counting reads in $BAM | |
} | |
BAMS=$( ls /users/asebe/aelek/proj/scATAC_nvec*/scATAC_pro/output*/mapping_result/*positionsort.bam ) | |
for BAM in $BAMS; do samtools_count "$BAM" & done | |
wait | |
echo "All done." | |
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