Public Git Hosting - GalaxyCodeBases.git/blob - BioInfo/BS-Seq/bwa-meth/compare/run-bsmooth.sh

1 . ./common.sh

5 # bsmooth won't let you specify abs path...

6 ## INDEX

7 #mkdir bsmooth

8 #perl $BSMOOTH/bin/bswc_bowtie2_index.pl --name=bsmooth/$(basename $REF .fa) $REF

10 mkdir -p results/

11 prog=bsmooth

BAM=results/bsmooth/$prog-$name.bam

rm -f logs/$prog-$name.err logs/$prog-$name.out

mkdir -p results/$prog/$name/ 

17 echo "

18 perl $BSMOOTH/bin/bswc_bowtie2_align.pl \

    --metrics results/$prog/$name-metrics.txt \

    --out results/$prog/$name/ \

21 --bam $BAM \

    -- bsmooth/$(basename $REF .fa) -- $REF \

23 -- --very-sensitive -p 8 -- $FQ1 -- $FQ2

samtools view -h $BAM.crick.bam | python src/bsmooth-adjust-crick.py | samtools view -bS - > $BAM.crick.fix.bam

java -jar $PICARD/MergeSamFiles.jar I=$BAM.watson.bam I=$BAM.crick.fix.bam O=$BAM AS=false " | bsub -J $prog-$name -e logs/$prog-$name.err -o logs/$prog-$name.out -n 12 -R "span[hosts=1]"

28 mkdir -p results/trim/bsmooth/

BAM=results/trim/bsmooth/$prog-$name.bam

rm -f logs/trim-$prog-$name.err logs/trim-$prog-$name.out

mkdir -p results/trim/$prog/$name/ 

32 echo "

33 perl $BSMOOTH/bin/bswc_bowtie2_align.pl \

34 --metrics results/trim/bsmooth/metrics.txt \

    --out results/trim/$prog/$name/ \

36 --bam $BAM \

    -- bsmooth/$(basename $REF .fa) -- $REF \

38 -- --very-sensitive -p 8 -- $TRIM_FQ1 -- $TRIM_FQ2

samtools view -h $BAM.crick.bam | python src/bsmooth-adjust-crick.py | samtools view -bS - > $BAM.crick.fix.bam

java -jar $PICARD/MergeSamFiles.jar I=$BAM.watson.bam I=$BAM.crick.fix.bam O=$BAM AS=false " | bsub -J trim-$prog-$name -e logs/trim-$prog-$name.err -o logs/trim-$prog-$name.out -n 12 -R "span[hosts=1]"