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slurm_circtools_detect_paired_mapping_old.sh
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#!/bin/bash
# @Author: Tobias Jakobi <tjakobi>
# @Date: Friday, May 6, 2016 4:10 PM
# @Email: tobias.jakobi@med.uni-heidelberg.de
# @Project: University Hospital Heidelberg, Section of Bioinformatics and Systems Cardiology
# @Last modified by: tjakobi
# @Last modified time: Friday, May 6, 2016 4:22 PM
# @License: CC BY-NC-SA
#SBATCH -n 1
#SBATCH -N 1
#SBATCH -c 40
#SBATCH --mem=250G
#SBATCH -J "circtools alignment"
#SBATCH --mail-type=END,FAIL,TIME_LIMIT_80
#SBATCH --mail-user=tobias.jakobi@med.uni-heidelberg.de
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=`expr ${2/$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/
mkdir -pv $4/$target/mate2_denovo/
mkdir -pv $4/$target/mate1_denovo/
OLD_PATH=`pwd`
# main mapping part
STAR --runThreadN 40 \
--genomeDir $1 \
--readFilesIn $2 $3 \
--readFilesCommand zcat \
--outFileNamePrefix $4/$target/ \
--outReadsUnmapped Fastx \
--outSJfilterOverhangMin 15 15 15 15 \
--alignSJoverhangMin 15 \
--alignSJDBoverhangMin 15 \
--outFilterMultimapNmax 20 \
--outFilterScoreMin 1 \
--outFilterMatchNmin 1 \
--outFilterMismatchNmax 2 \
--chimSegmentMin 15 \
--chimScoreMin 15 \
--chimScoreSeparation 10 \
--chimJunctionOverhangMin 15 \
--chimOutType Junctions SeparateSAMold\
--sjdbGTFfile $6
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 \
# --readFilesIn $4/$target/Unmapped.out.mate1.gz \
# --readFilesCommand zcat \
# --outFileNamePrefix $4/$target/mate1/ \
# --outReadsUnmapped Fastx \
# --outSJfilterOverhangMin 15 15 15 15 \
# --alignSJoverhangMin 15 \
# --alignSJDBoverhangMin 15 \
# --seedSearchStartLmax 30 \
# --outFilterMultimapNmax 20 \
# --outFilterScoreMin 1 \
# --outFilterMatchNmin 1 \
# --outFilterMismatchNmax 2 \
# --chimSegmentMin 15 \
# --chimScoreMin 15 \
# --chimScoreSeparation 10 \
# --chimJunctionOverhangMin 15 \
# --chimOutType Junctions SeparateSAMold\
# --sjdbGTFfile $6
#
# 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
#
# cd $OLD_PATH
#
# ## done with mate1 mapping
#
# ## mapping mate2 now
#
# STAR --runThreadN 40 \
# --genomeDir $1 \
# --readFilesIn $4/$target/Unmapped.out.mate2.gz \
# --readFilesCommand zcat \
# --outFileNamePrefix $4/$target/mate2/ \
# --outReadsUnmapped Fastx \
# --outSJfilterOverhangMin 15 15 15 15 \
# --alignSJoverhangMin 15 \
# --alignSJDBoverhangMin 15 \
# --seedSearchStartLmax 30 \
# --outFilterMultimapNmax 20 \
# --outFilterScoreMin 1 \
# --outFilterMatchNmin 1 \
# --outFilterMismatchNmax 2 \
# --chimSegmentMin 15 \
# --chimScoreMin 15 \
# --chimScoreSeparation 10 \
# --chimJunctionOverhangMin 15 \
# --chimOutType Junctions SeparateSAMold\
# --sjdbGTFfile $6
#
# 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
# cd $OLD_PATH
# done with mate 2 mapping
## map from scratch
STAR --runThreadN 40 \
--genomeDir $1 \
--readFilesIn $2 \
--readFilesCommand zcat \
--outFileNamePrefix $4/$target/mate1_denovo/ \
--outReadsUnmapped Fastx \
--outSJfilterOverhangMin 15 15 15 15 \
--alignSJoverhangMin 15 \
--alignSJDBoverhangMin 15 \
--seedSearchStartLmax 30 \
--outFilterMultimapNmax 20 \
--outFilterScoreMin 1 \
--outFilterMatchNmin 1 \
--outFilterMismatchNmax 2 \
--chimSegmentMin 15 \
--chimScoreMin 15 \
--chimScoreSeparation 10 \
--chimJunctionOverhangMin 15 \
--chimOutType Junctions SeparateSAMold\
--sjdbGTFfile $6
cd $4/$target/mate1_denovo/
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
STAR --runThreadN 40 \
--genomeDir $1 \
--readFilesIn $3 \
--readFilesCommand zcat \
--outFileNamePrefix $4/$target/mate2_denovo/ \
--outReadsUnmapped Fastx \
--outSJfilterOverhangMin 15 15 15 15 \
--alignSJoverhangMin 15 \
--alignSJDBoverhangMin 15 \
--seedSearchStartLmax 30 \
--outFilterMultimapNmax 20 \
--outFilterScoreMin 1 \
--outFilterMatchNmin 1 \
--outFilterMismatchNmax 2 \
--chimSegmentMin 15 \
--chimScoreMin 15 \
--chimScoreSeparation 10 \
--chimJunctionOverhangMin 15 \
--chimOutType Junctions SeparateSAMold\
--sjdbGTFfile $6
cd $4/$target/mate2_denovo/
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