I was wondering if you could clarify how best to deal with non-canonical splice sites when assembling long-read ONT data, please. My organism uses a wide range of splice sites, both canonical and non-canonical. I've aligned my ONT reads with minimap2 without penalizing non-canonical splice sites:
minimap2 -a -x splice -un -C0 --junc-bed
I am unsure whether I should be using the --viral option in stringtie2 or not. Does the default mode ignore non-canonical splice sites altogether? Or, in other words, is the --viral option designed for cases where all splice sites are expected to be non canonical? I would be grateful for clarification on how the --viral option operates, please.
Hello,
I was wondering if you could clarify how best to deal with non-canonical splice sites when assembling long-read ONT data, please. My organism uses a wide range of splice sites, both canonical and non-canonical. I've aligned my ONT reads with minimap2 without penalizing non-canonical splice sites:
minimap2 -a -x splice -un -C0 --junc-bedI am unsure whether I should be using the
--viraloption in stringtie2 or not. Does the default mode ignore non-canonical splice sites altogether? Or, in other words, is the--viraloption designed for cases where all splice sites are expected to be non canonical? I would be grateful for clarification on how the--viraloption operates, please.Thank you very much!
Best wishes, Marius