Is there any relevant evaluation for winnowmap2 with RNA-Seq data (like ont, iso-seq)?

[shengxinzhuan]

Hello, I've been using ONT's full-length transcript data for genome annotation recently, but it seems that minimap2 doesn't handle some complex regions very well. I had a great experience using winowmap for mapping HiFi data before, so I wanted to ask if winnowmap2 has specific parameters or modes for RNA-Seq data like this?

[keenhl]

I think the map_ont should work for this.

-x STR preset (always applied before other options) []
- map-ont (ont-to-ref, uses default param)
- map-pb (hifi-to-ref, all defaults but does finer read fragmentation in SV-aware mapping)
- map-pb-clr (clr-to-ref, sets --sv-off)
- splice/splice:hq - long-read/Pacbio-CCS spliced alignment, sets --sv-off
- asm5/asm10/asm20 - asm-to-ref mapping