Add unique cell identifiers, merge and split bams.

sinto.sh

#!/bin/bash
#$ -N sinto
#$ -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 sinto.out
#$ -pe smp 16
#$ -j y

NCORE=16
WDIR="/users/asebe/aelek/proj/Ptf1A/scATAC/sinto"
NAMES="e10_WT e10_KO e13_KO_Sept2020 e13_WT_July2020"
OUTDIR="bam"
OUTBAM=$OUTDIR"/Ptf1A.RG.bam"
CELLS="../txt/CIClusters.txt"
BARCODE="CI"
SAMTOOLS_PATH="/users/asebe/aelek/bin/samtools-1.12"

sinto_addtags () {
  local NAME=$1
  local BAM=../CellRanger/$NAME/outs/possorted_bam.bam
  local OUTPUT=bam/$NAME.bam
  local TAGFILE=../txt/$NAME.txt
  echo $(date): Adding tags to $BAM
  sinto addtags -p $NCORE -b $BAM -f $TAGFILE -o $OUTPUT
  echo $(date): Added tags to $OUTPUT
}
echo $(date): Starting
cd $WDIR
mkdir $OUTDIR
for NAME in $NAMES; do sinto_addtags "$NAME" & done
wait
BAMS=$( ls $OUTDIR/*bam )
for BAM in $BAMS; do
  echo $(date): Indexing $BAM
  ${SAMTOOLS_PATH}/samtools index -@ $NCORE $BAM
  echo $(date): Getting header from $BAM
  RG=${BAM%%bam}txt
  ${SAMTOOLS_PATH}/samtools view -H $BAM | grep '@RG' > $RG
done
wait
echo $(date): Merging bams
${SAMTOOLS_PATH}/samtools view -H $BAM | grep '@RG' -v > $OUTDIR/header.txt
RGS=$( ls bam/*txt)
cat $RGS >> $OUTDIR/header.txt
${SAMTOOLS_PATH}/samtools merge -@ $NCORE -h $HEADER $OUTBAM $BAMS
${SAMTOOLS_PATH}/samtools index -@ $NCORE $OUTBAM
echo $(date): Filtering barcodes
sinto filterbarcodes -b $OUTBAM -c $CELLS --barcodetag $BARCODE
echo $(date): Done!