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BrooksLabUCSC / flair

Full-Length Alternative Isoform analysis of RNA
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FLAIR missing isoforms #340

Open lilif99 opened 1 month ago

lilif99 commented 1 month ago

Hello,

I am trying to use FLAIR to look at transcript isoforms of FCGR2C with Nanopore cDNA sequencing. FLAIR appears to be failing to pick up isoforms showing retention of the final intron (which IGV shows has quite a few supporting reads) despite picking up the much less common retention of intron 3.

Is there a reason that FLAIR is missing this isoform? Any advice would be appreciated, thank you!

IGV

FLAIR

lilif99 commented 1 month ago

Sorry it didn't attach to the original post- this is my flair output FLAIR