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adnaniazi / tailfindr

An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
https://www.cbu.uib.no/valen/
GNU General Public License v3.0
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NAs in polyA tail length estimation #16

Closed ahorvath closed 3 years ago

ahorvath commented 3 years ago

Dear @adnaniazi,

What do NAs most likely represent in the polyA tail estimation? Can we speculate that they are typically longer or sorter than the population?

Thanks for developing this great package.

Best, Attila

adnaniazi commented 3 years ago

Dear Attila,

Thanks for using tailfindr.

NAs in tail length estimation in majority of cases means that there was no polyA-tail-like region found in the squiggle in the beginning for the RNA read. Wrong segmentation from MinION can sometimes generate such kinds of reads. In minority of cases, NAs might also be due to failure of tailfindr algorithm itself, but those are very rare; majority of NAs come from there not being a polyA like region in the raw Nanopore signal.

Hope this helps!

Best, Adnan

ahorvath commented 3 years ago

Sounds great. Actually, this would make much sense biologically in some of our conditions (transcripts having no or very short polyA tail).

Thanks for your prompt and professional answer!