#!/bin/bash #map .bax.h5 files from individual PacBio cells to Release 5 using blasr echo "mapping .bax.h5 files to Release 5" samples=() for input in `ls Dro*/*/*/*bax.h5` do sample=`basename $input .bax.h5` output1="${sample}.sam" output2="${sample}.unaligned" qsub -l cores=12 -V -b y -cwd -N blasr_${sample} "install/smrtanalysis-2.1.1.128549/analysis/bin/blasr $input dm3.fa -bestn 1 -nproc 12 -minPctIdentity 80 -sam -out $output1 -unaligned $output2" qsub -V -b y -cwd -N sort_${sample} -hold_jid blasr_${sample} "install/smrtanalysis-2.1.1.128549/analysis/bin/samtools view -bS $output1 | install/smrtanalysis-2.1.1.128549/analysis/bin/samtools sort - $sample" samples+=(sort_${sample}) done #merge bam files from individual cells and index merged bam file echo "merging and indexing bam files" holdlist=`printf -- '%s,' "${samples[@]}"` input="m131*_p0*.bam" output="dm3PacBio.bam" qsub -V -b y -cwd -N merge_pacbio -hold_jid $holdlist "install/smrtanalysis-2.1.1.128549/analysis/bin/samtools merge $output $input" qsub -V -b y -cwd -N index_pacbio -hold_jid merge_pacbio "install/smrtanalysis-2.1.1.128549/analysis/bin/samtools index $output" #merge unmapped reads and remove .sam, .bam and .unaligned files from individual cells echo "merging unmapped reads and cleaning up" qsub -V -b y -cwd -N merge_unmapped -hold_jid index_pacbio "cat m131*unaligned > dm3PacBio.unaligned" qsub -V -b y -cwd -N rm_cell_files -hold_jid merge_unmapped "rm m131*unaligned m131*bam m131*sam"