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slurm_circtools_detect_paired_mapping_make.sh
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#!/bin/bash
# @Author: Tobias Jakobi <tjakobi>
# @Email: [email protected]
# @Project: University Hospital Heidelberg, Section of Bioinformatics and Systems Cardiology
# @License: CC BY-NC-SA
#SBATCH -n 1
#SBATCH -N 1
#SBATCH -p long
#SBATCH -c 40
#SBATCH --mem=250G
#SBATCH -J "circtools alignment"
#SBATCH --mail-type=END,FAIL,TIME_LIMIT_80
#SBATCH [email protected]
#module load star
# check if we have 6 arguments
if [ ! $# == 6 ]; then
echo "Usage: $0 [STAR index] [Read 1 file] [Read 2 file] [target dir e.g. /tmp/] [Read 1 marker, e.g. R1] [GTF file]"
exit
fi
# $1 -> Genome index
# $2 -> Read 1
# $3 -> Read 2
# $4 -> Target directory
# remove the file extension and potential "R1" markings
# (works for double extension, e.g. .fastq.gz)
target=$5
# create the target directory, STAR will not do that for us
mkdir -pv $4/$target
mkdir -pv $4/$target/mate1/
mkdir -pv $4/$target/mate2/
# create random string
TMP_RND=`cat /dev/urandom | tr -dc 'a-zA-Z0-9' | fold -w 10 | head -n 1`
#mkdir -pv /scratch/global_tmp/${TMP_RND}_${target}
#mkdir -pv /scratch/global_tmp/${TMP_RND}_${target}_mate1
#mkdir -pv /scratch/global_tmp/${TMP_RND}_${target}_mate2
OLD_PATH=`pwd`
# main mapping part
STAR --runThreadN 40\
--genomeDir $1\
--genomeLoad NoSharedMemory\
--outTmpDir /scratch/global_tmp/${TMP_RND}_${target}/\
--readFilesIn $2 $3\
--readFilesCommand zcat\
--outFileNamePrefix $4/$target/\
--outReadsUnmapped Fastx\
--outSAMattributes NH HI AS nM NM MD jM jI XS\
--outSJfilterOverhangMin 15 15 15 15\
--outFilterMultimapNmax 20\
--chimMultimapNmax 20\
--outFilterScoreMin 1\
--outFilterMatchNminOverLread 0.7\
--outFilterMismatchNmax 999\
--outFilterMismatchNoverLmax 0.05\
--alignIntronMin 20\
--alignIntronMax 1000000\
--alignMatesGapMax 1000000\
--alignSJoverhangMin 15\
--alignSJDBoverhangMin 10\
--alignSoftClipAtReferenceEnds No\
--chimSegmentMin 15\
--chimScoreMin 15\
--chimScoreSeparation 10\
--chimJunctionOverhangMin 15\
--sjdbGTFfile $6\
--quantMode GeneCounts\
--twopassMode Basic\
--chimOutType Junctions
cd $4/$target
gzip Unmapped.out.mate1
gzip Unmapped.out.mate2
awk 'BEGIN {OFS="\t"} {split($6,C,/[0-9]*/); split($6,L,/[SMDIN]/); if (C[2]=="S") {$10=substr($10,L[1]+1); $11=substr($11,L[1]+1)}; if (C[length(C)]=="S") {L1=length($10)-L[length(L)-1]; $10=substr($10,1,L1); $11=substr($11,1,L1); }; gsub(/[0-9]*S/,"",$6); print}' Aligned.out.sam > Aligned.noS.sam
#awk 'BEGIN {OFS="\t"} {split($6,C,/[0-9]*/); split($6,L,/[SMDIN]/); if (C[2]=="S") {$10=substr($10,L[1]+1); $11=substr($11,L[1]+1)}; if (C[length(C)]=="S") {L1=length($10)-L[length(L)-1]; $10=substr($10,1,L1); $11=substr($11,1,L1); }; gsub(/[0-9]*S/,"",$6); print}' Chimeric.out.sam > Chimeric.noS.sam
grep "^@" Aligned.out.sam > header.txt
rm -f Aligned.out.sam
#rm -f Chimeric.out.sam
rm -f -r _STARgenome
rm -f -r _STARpass1
samtools view -bS Aligned.noS.sam | samtools sort -@ 10 -m 2G -T tempo -o Aligned.noS.bam /dev/stdin
samtools reheader header.txt Aligned.noS.bam > Aligned.noS.tmp
mv Aligned.noS.tmp Aligned.noS.bam
samtools index Aligned.noS.bam
#samtools view -bS Chimeric.noS.sam | samtools sort -@ 10 -m 2G -T tempo -o Chimeric.noS.bam /dev/stdin
#samtools reheader header.txt Chimeric.noS.bam > Chimeric.noS.tmp
#mv Chimeric.noS.tmp Chimeric.noS.bam
#samtools index Chimeric.noS.bam
rm -f Aligned.noS.sam
#rm -f Chimeric.noS.sam
cd $OLD_PATH
## done with main mapping
## mapping mate1 now
STAR --runThreadN 40\
--genomeDir $1\
--genomeLoad NoSharedMemory\
--outTmpDir /scratch/global_tmp/${TMP_RND}_${target}_mate1/\
--readFilesIn $4/$target/Unmapped.out.mate1.gz\
--readFilesCommand zcat\
--outFileNamePrefix $4/$target/mate1/ \
--outReadsUnmapped Fastx\
--outSAMattributes NH HI AS nM NM MD jM jI XS\
--outSJfilterOverhangMin 15 15 15 15\
--outFilterMultimapNmax 20\
--chimMultimapNmax 20\
--outFilterScoreMin 1\
--outFilterMatchNminOverLread 0.7\
--outFilterMismatchNmax 999\
--outFilterMismatchNoverLmax 0.05\
--alignIntronMin 20\
--alignIntronMax 1000000\
--alignMatesGapMax 1000000\
--alignSJoverhangMin 15\
--alignSJDBoverhangMin 10\
--alignSoftClipAtReferenceEnds No\
--chimSegmentMin 15\
--chimScoreMin 15\
--chimScoreSeparation 10\
--chimJunctionOverhangMin 15\
--sjdbGTFfile $6\
--quantMode GeneCounts\
--twopassMode Basic\
--chimOutType Junctions
cd $4/$target/mate1/
awk 'BEGIN {OFS="\t"} {split($6,C,/[0-9]*/); split($6,L,/[SMDIN]/); if (C[2]=="S") {$10=substr($10,L[1]+1); $11=substr($11,L[1]+1)}; if (C[length(C)]=="S") {L1=length($10)-L[length(L)-1]; $10=substr($10,1,L1); $11=substr($11,1,L1); }; gsub(/[0-9]*S/,"",$6); print}' Aligned.out.sam > Aligned.noS.sam
#awk 'BEGIN {OFS="\t"} {split($6,C,/[0-9]*/); split($6,L,/[SMDIN]/); if (C[2]=="S") {$10=substr($10,L[1]+1); $11=substr($11,L[1]+1)}; if (C[length(C)]=="S") {L1=length($10)-L[length(L)-1]; $10=substr($10,1,L1); $11=substr($11,1,L1); }; gsub(/[0-9]*S/,"",$6); print}' Chimeric.out.sam > Chimeric.noS.sam
grep "^@" Aligned.out.sam > header.txt
rm -f Aligned.out.sam
#rm -f Chimeric.out.sam
rm -f -r _STARgenome
rm -f -r _STARpass1
samtools view -bS Aligned.noS.sam | samtools sort -@ 10 -m 2G -T tempo -o Aligned.noS.bam /dev/stdin
samtools reheader header.txt Aligned.noS.bam > Aligned.noS.tmp
mv Aligned.noS.tmp Aligned.noS.bam
samtools index Aligned.noS.bam
#samtools view -bS Chimeric.noS.sam | samtools sort -@ 10 -m 2G -T tempo -o Chimeric.noS.bam /dev/stdin
#samtools reheader header.txt Chimeric.noS.bam > Chimeric.noS.tmp
#mv Chimeric.noS.tmp Chimeric.noS.bam
#samtools index Chimeric.noS.bam
rm -f Aligned.noS.sam
#rm -f Chimeric.noS.sam
gzip Unmapped.out.mate1
cd $OLD_PATH
## done with mate1 mapping
## mapping mate2 now
STAR --runThreadN 40\
--genomeDir $1\
--genomeLoad NoSharedMemory\
--outTmpDir /scratch/global_tmp/${TMP_RND}_${target}_mate2/\
--readFilesIn $4/$target/Unmapped.out.mate2.gz\
--readFilesCommand zcat\
--outFileNamePrefix $4/$target/mate2/ \
--outReadsUnmapped Fastx\
--outSAMattributes NH HI AS nM NM MD jM jI XS\
--outSJfilterOverhangMin 15 15 15 15\
--outFilterMultimapNmax 20\
--chimMultimapNmax 20\
--outFilterScoreMin 1\
--outFilterMatchNminOverLread 0.7\
--outFilterMismatchNmax 999\
--outFilterMismatchNoverLmax 0.05\
--alignIntronMin 20\
--alignIntronMax 1000000\
--alignMatesGapMax 1000000\
--alignSJoverhangMin 15\
--alignSJDBoverhangMin 10\
--alignSoftClipAtReferenceEnds No\
--chimSegmentMin 15\
--chimScoreMin 15\
--chimScoreSeparation 10\
--chimJunctionOverhangMin 15\
--sjdbGTFfile $6\
--quantMode GeneCounts\
--twopassMode Basic\
--chimOutType Junctions
cd $4/$target/mate2/
awk 'BEGIN {OFS="\t"} {split($6,C,/[0-9]*/); split($6,L,/[SMDIN]/); if (C[2]=="S") {$10=substr($10,L[1]+1); $11=substr($11,L[1]+1)}; if (C[length(C)]=="S") {L1=length($10)-L[length(L)-1]; $10=substr($10,1,L1); $11=substr($11,1,L1); }; gsub(/[0-9]*S/,"",$6); print}' Aligned.out.sam > Aligned.noS.sam
#awk 'BEGIN {OFS="\t"} {split($6,C,/[0-9]*/); split($6,L,/[SMDIN]/); if (C[2]=="S") {$10=substr($10,L[1]+1); $11=substr($11,L[1]+1)}; if (C[length(C)]=="S") {L1=length($10)-L[length(L)-1]; $10=substr($10,1,L1); $11=substr($11,1,L1); }; gsub(/[0-9]*S/,"",$6); print}' Chimeric.out.sam > Chimeric.noS.sam
grep "^@" Aligned.out.sam > header.txt
rm -f Aligned.out.sam
#rm -f Chimeric.out.sam
rm -f -r _STARgenome
rm -f -r _STARpass1
samtools view -bS Aligned.noS.sam | samtools sort -@ 10 -m 2G -T tempo -o Aligned.noS.bam /dev/stdin
samtools reheader header.txt Aligned.noS.bam > Aligned.noS.tmp
mv Aligned.noS.tmp Aligned.noS.bam
samtools index Aligned.noS.bam
#samtools view -bS Chimeric.noS.sam | samtools sort -@ 10 -m 2G -T tempo -o Chimeric.noS.bam /dev/stdin
#samtools reheader header.txt Chimeric.noS.bam > Chimeric.noS.tmp
#mv Chimeric.noS.tmp Chimeric.noS.bam
#samtools index Chimeric.noS.bam
rm -f Aligned.noS.sam
#rm -f Chimeric.noS.sam
gzip Unmapped.out.mate1
# remove tmp dirs
rm /scratch/global_tmp/${TMP_RND}_${target}/ -rf
rm /scratch/global_tmp/${TMP_RND}_${target}_mate1/ -rf
rm /scratch/global_tmp/${TMP_RND}_${target}_mate2/ -rf