Does DNAscent handle supplementary alignments the same as primary alignments?

MBoemo / DNAscent

Software for detecting regions of BrdU and EdU incorporation in Oxford Nanopore reads.

https://www.boemogroup.org/

GNU General Public License v3.0

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Does DNAscent handle supplementary alignments the same as primary alignments? #74

Closed ywang285 closed 1 week ago

ywang285 commented 2 weeks ago

Hi, I am working on a bam file in which each read has on average 20 supplementary alignments. I found somehow MM ML tags in supplementary alignments cannot be correctly handled by dorado aligner default setting, but below minimap2 alignment command seems work: minimap2 -x map-ont -a -t ${num_threads} -y --secondary=no -Y ${REFERENCE} I wonder if I use a bam file aligned using the above command as DNAscent detect input, would there be any issue you can foresee? Thanks!

MBoemo commented 1 week ago

Sorry for the late reply. Just to check my understanding: you don't want to use these secondary alignments, hence why you're suppressing them with --secondary=no? If that's correct then there shouldn't be any issues.