Tweaking minimap2 parameters in Isoquant

ablab / IsoQuant

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

https://ablab.github.io/IsoQuant/

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Tweaking minimap2 parameters in Isoquant #246

Open sanyalab opened 3 days ago

sanyalab commented 3 days ago

Hi Andrey,

I might have missed it, but is there a way to tweak the minimap2 parameters in IsoQuant? and also adding support for other aligners like GMAP and uLTRA?

Thanks Abhijit

andrewprzh commented 2 days ago

Dear @sanyalab

In general, IsoQuant was optimized for minimap2, and in my experience minimap2 shows optimal combination of computational performance and mapping quality. At the moment there is no way to change minimap2 parameters or specify other aligner via command line. However, IsoQuant supports BAM files as input, thus a user can provide a custom BAM file generated by any aligner.

Best Andrey