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BrooksLabUCSC / flair

Full-Length Alternative Isoform analysis of RNA
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assign reads into isoforms without mapping #211

Closed xieyy46 closed 2 years ago

xieyy46 commented 2 years ago

Hi flair team! I wonder if I can assign reads into isoforms without using the minimap2 mapping step? As you konw, I have mapped my reads to genome before using flair. What I want to do is grouping reads into isoforms whatever new isoforms or annotated isoforms from GTF.

Jeltje commented 2 years ago

I'm not sure I understand the question. If you want to assign reads to isoforms, you need to do a mapping step at some point. Either you align the reads to the genome (that's what flair align does) and then use the coordinates to map them to the isoform coordinates, or you align the reads to the transcripts (which is in part what flair collapse does).

Can you be a bit more specific? What is your end goal?

Jeltje commented 2 years ago

Please reopen this ticket if you have more information