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a-slide / NanoCount

EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
https://a-slide.github.io/NanoCount/
MIT License
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Nanocount vs Flair #28

Closed sagnikbanerjee15 closed 10 months ago

sagnikbanerjee15 commented 11 months ago

Hello,

I am using Nanocount to estimate expression levels. I found that Flair quantifies the transcripts after finding novel ones. Is it sufficient to accept the results of Flair quantify or is it necessary to execute Nanocount?

Thank you

josiegleeson commented 10 months ago

Hi,

It's up to you really, but we benchmarked NanoCount with FLAIR and found that NanoCount performed better and removed some false positive novel transcripts. So I would recommend parsing the output from FLAIR into NanoCount for quantification.

Hope this helps.

sagnikbanerjee15 commented 5 months ago

Hello,

Thanks for the reply. I was comparing the counts from FLAIR with Nanocounts and I found that several transcripts had a difference of over 500 counts. Could there be any reason for that difference?

Thank you.

josiegleeson commented 5 months ago

Hi, FLAIR may have found novel isoforms that have incorrect 3' ends, and NanoCount can then remove these incorrect isoforms (by assigning them 0 counts). They also likely use different quantification algorithms so both of these are likely causing the differences. Thanks.