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ZijieJin / scFusion

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SMART-seq2 with read length less than 60 bp #18

Closed cbiagii closed 1 year ago

cbiagii commented 1 year ago

First of all, thank you so much for such a comprehensive and helpful pipeline!

I'm trying to run on the data I have (SMART-seq2) and I'm having problems in the FusionCandidate step. My samples have reads with a length of 38 bp, so when I get to the FusionCandidate step I get the error below: ValueError: could not broadcast input array from shape (39,) into shape (61,)

I would like to know if you have any suggestions for running scFusion in this case, where my reads are smaller than 60 bp but are SMART-seq.

Thank you very much for your help!

ZijieJin commented 1 year ago

I do not recommend you applying scFusion to this dataset. The read is too short to detect gene fusions, or the sensitivity might be very low

cbiagii commented 1 year ago

Thanks a lot for you reply!