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splicebox / PsiCLASS

Simultaneous multi-sample transcript assembler for RNA-seq data
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Requesting information about usage in long-reads #36

Open sagnikbanerjee15 opened 3 months ago

sagnikbanerjee15 commented 3 months ago

Hello,

Is it possible for PsiClass to be executed on long-reads generated from PacBio and/or Nanopore? If not, is it possible to make quick modifications to the code to adapt to long reads?

Thank you, Sagnik

mourisl commented 3 months ago

I think it should be able to handle the long-read alignment BAM file. If the intron splice site is more or less accurate, it should be fine. The potential issue I can think of from the long read is that a read can span multiple exons, and by default, PsiCLASS stores at most 127 exons for an alignment, and may crash when it goes above. You can change the threshold by increase the threshold here https://github.com/splicebox/PsiCLASS/blob/master/defs.h#L6 .

sagnikbanerjee15 commented 3 months ago

Thank you for the quick reply. I aligned the long reads using minimap2 and am using addXS but I am entering into a segmentation fault. I have tried increasing the max number of alignments to 255 but that has not solved the problem.

Thank you.