gravatar for prameelaawale

2 hours ago by

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

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.

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