Parsing of the X CIGAR code in bam files

NBISweden / AGAT

Another Gtf/Gff Analysis Toolkit

GNU General Public License v3.0

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Parsing of the X CIGAR code in bam files #422

Closed sanyalab closed 4 months ago

sanyalab commented 4 months ago

Hello,

Can agat_convert_minimap2_bam2gff.pl be modified to process the X CIGAR code in some BAM files? I have aligned IsoSeq data to genome with minimap and I have a bam file with the =/X CIGAR code. After conversion to GFF I cannot see the percent identity and coverage of the IsoSeq mRNA on the genome, like I do for a GMAP output.

Can the code be modified to handle the X CIGAR class?

Thanks Abhijit

Juke34 commented 4 months ago

Sure, but I would need a detailed example to be sure to implement it properly

sanyalab commented 4 months ago

Hi Jacques,

Thank you for replying and agreeing to implement. I am working on a different project for now, so closing this request temporarily. Will re-open once I have data, examples and objectives to share. Thanks

-Abhijit