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iMetOsaka / UNAGI

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No strand infomation for the final output #7

Open zjzace opened 2 years ago

zjzace commented 2 years ago

Dear Nicolas,

I have tried to run UNAGI on my own nanopore data. I run it successufully without error. However, I cannot got the strand infomation in the final output (both 'Splicing_Isoforms.bed' and 'Splicing_Isoforms_Unique.bed'). Can you help to check?

Leo

JungNicolas commented 2 years ago

Hello Leo.

First of all, sorry for the delay in answering you. The splice sites information is generated using both positively and negatively stranded coverage. The data is also filtered by using the combined coverage of both strands. As such, it looses the stranding information in the process.

An update to allow the search of isoforms individually for positively stranded and negatively stranded reads is possible, but it will yield less of them because of the filtering by coverage. Let me know if this is a feature you would be interested in.

Nicolas.