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slurm_circtools_detect_mapping.sh
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#!/bin/bash
# @Author: Tobias Jakobi <tjakobi>, Tomas Germade <tgermade>
# @Date: Friday, June 14, 2019 17:55
# @Email: [email protected], [email protected]
# @Project: MSc Semester Project, ETH Zuerich, Laboratory of Systems Neuroscience
# @Last modified by: tgermade
# @Last modified time: Friday, June 14, 2019 17:55
# @License: CC BY-NC-SA
#SBATCH -n 1
#SBATCH -N 1
#SBATCH -c 12
#SBATCH --mem=250G
#SBATCH -J "circtools alignment"
#SBATCH --mail-type=END,FAIL,TIME_LIMIT_80
#SBATCH [email protected]
# check number of arguments to display help
case $# in 5|7) ;;
*)
echo "Usage paired: $0 [STAR index] [target dir] [gene annotation GTF file] [thread number] [Read 1 file] [Read 2 file] [Read 1 marker, e.g. R1]"
echo "Usage unpaired: $0 [STAR index] [target dir] [gene annotation GTF file] [thread number] [Read]"
exit
esac
# $1 -> Genome index
# $2 -> target directory
# $3 -> gene annotation file
# $4 -> number of threads to use
# $5 -> read / read 1
# $6 -> read 2
# $7 -> read 1 marker
# remove the file extension and potential "R1" markings
# (works for double extension, e.g. .fastq.gz)
if [ $# = 5 ]; then
format="unpaired" &&
target=`echo $5 | sed "s%\.fastq\.gz$%%"` &&
# create the target directory, STAR will not do that for us
mkdir -pv $2/$target
elif [ $# = 7 ]; then
format="paired" &&
target=`expr ${5/$7/} : '\(.*\)\..*\.'` &&
#target=`echo $5 | sed "s%\.fastq\.gz$%%;s%$7%%"` &&
# create the target directory, STAR will not do that for us
mkdir -pv $2/$target &&
mkdir -pv $2/$target/mate1/ &&
mkdir -pv $2/$target/mate2/
fi
OLD_PATH=`pwd`
# main mapping part
# Run on unpaired data
if [ $format = "unpaired" ]; then
STAR --runThreadN $4\
--genomeDir $1\
--genomeLoad NoSharedMemory\
--readFilesIn $5\
--readFilesCommand zcat\
--outFileNamePrefix $2/$target/\
--outReadsUnmapped Fastx\
--outSAMattributes NH HI AS nM NM MD jM jI XS\
--outSJfilterOverhangMin 15 15 15 15\
--outFilterMultimapNmax 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 $3\
--quantMode GeneCounts\
--twopassMode Basic\
--chimOutType Junctions SeparateSAMold &&
cd $2/$target &&
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
# Run on paired data
elif [ $format = "paired" ]; then
STAR --runThreadN $4\
--genomeDir $1\
--genomeLoad NoSharedMemory\
--readFilesIn $5 $6\
--readFilesCommand zcat\
--outFileNamePrefix $2/$target/\
--outReadsUnmapped Fastx\
--outSAMattributes NH HI AS nM NM MD jM jI XS\
--outSJfilterOverhangMin 15 15 15 15\
--outFilterMultimapNmax 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 $3\
--quantMode GeneCounts\
--twopassMode Basic\
--chimOutType Junctions SeparateSAMold
cd $2/$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 $4\
--genomeDir $1\
--genomeLoad NoSharedMemory\
--readFilesIn $2/$target/Unmapped.out.mate1.gz\
--readFilesCommand zcat\
--outFileNamePrefix $2/$target/mate1/ \
--outReadsUnmapped Fastx\
--outSAMattributes NH HI AS nM NM MD jM jI XS\
--outSJfilterOverhangMin 15 15 15 15\
--outFilterMultimapNmax 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 $3\
--quantMode GeneCounts\
--twopassMode Basic\
--chimOutType Junctions SeparateSAMold
cd $2/$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
cd $OLD_PATH
## done with mate1 mapping
## mapping mate2 now
STAR --runThreadN $4\
--genomeDir $1\
--genomeLoad NoSharedMemory\
--readFilesIn $2/$target/Unmapped.out.mate2.gz\
--readFilesCommand zcat\
--outFileNamePrefix $2/$target/mate2/ \
--outReadsUnmapped Fastx\
--outSAMattributes NH HI AS nM NM MD jM jI XS\
--outSJfilterOverhangMin 15 15 15 15\
--outFilterMultimapNmax 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 $3\
--quantMode GeneCounts\
--twopassMode Basic\
--chimOutType Junctions SeparateSAMold
cd $2/$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
fi