Dear all,
I would like to ask for some help with samtools:
I found many threads about using samtools to filter reads based on some criteria, however, I did not find any clue how to filter reads based on the CIGAR value.
How can I filter reads (from a BAM) from RNA-seq files that are non-splitted / non-gapped?
From one BAM, I would like to have two BAMs ne with gapped reads and one with non-gapped reads.
Could someone write an example?
Thank you for the help in advance,
I would like to ask for some help with samtools:
I found many threads about using samtools to filter reads based on some criteria, however, I did not find any clue how to filter reads based on the CIGAR value.
How can I filter reads (from a BAM) from RNA-seq files that are non-splitted / non-gapped?
From one BAM, I would like to have two BAMs ne with gapped reads and one with non-gapped reads.
Could someone write an example?
Thank you for the help in advance,
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