Extracting Split read alignments
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2.4 years ago

I am trying to extract the split read alignments with bwa-mem for pair end sequencing. This is my code.

# Extract the split-read alignments

samtools view -h rscm2.bam \
| scripts/extractSplitReads_BwaMem -i stdin \
| samtools view -Sb - \
> rscm2.splitters.unsorted.bam


But I am getting this error message. /cm/local/apps/slurm/var/spool/job16557014/slurm_script: line 18: scripts/extractSplitReads_BwaMem: No such file or directory Can anyone please help to fix this error? Thank you in advance.

alignment • 823 views
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does the directory 'scripts' exists in the current directory ? try to use a full path for scripts/extractSplitReads_BwaMem instead of a relative path ?