Best minimap2 parameters for use with bambu

GoekeLab / bambu

Reference-guided transcript discovery and quantification for long read RNA-Seq data

GNU General Public License v3.0

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Best minimap2 parameters for use with bambu #442

Closed rob-p closed 3 months ago

rob-p commented 3 months ago

Hi Bambu team,

Thanks for the great software! We (@zzare-umd, @NPSDC and I) were curious if there are any particular parameters you suggest when aligning with minimap2 prior to bambu. We saw that you may want to pass -uf when aligning direct RNA data (https://github.com/GoekeLab/bambu/issues/232), but does it ever make sense to modify the default -N or -p parameters? Will bambu consider genomic multimapping reads if equally-good alignments exist?

Thanks! Rob, Zahra, and Noor

cying111 commented 3 months ago

Hi @rob-p, @zzare-umd, @NPSDC,

Thank you for your kind words! We're glad that you like the software. Currently, Bambu relies on minimap2 to choose among equally good alignments by filtering out secondary alignments. Therefore, the parameters -N and -p are expected to have no impact on the results, as all secondary alignments will be filtered out.

Hope this clarifies your question! Thank you and all the best, Warm regards, Ying

rob-p commented 3 months ago

Hi @cying111,

Yes; this helps a lot. Thanks for the quick response and congrats again on the nice tool!

Best, Rob