JUM a lot of error... but finish runnnig an output empty file.

qqwang-berkeley / JUM

A tool for annotation-free differential analysis of tissue-specific pre-mRNA alternative splicing patterns

MIT License

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JUM a lot of error... but finish runnnig an output empty file. #45

Closed rLannes closed 1 year ago

rLannes commented 1 year ago

I am trying to run JUM on a custom genome. I don't really understand what I did wrong, any help appreciated. Because the genome is really fragmented, I only kept the read that align over contig >100kb

JUM_log.txt

The log is quite long. I attached it

after double checking I believe my refFlat format is incorrect. Does that would explain the absence of results from JUM_C? But I don't understand why I got so much error message before this step....

rLannes commented 1 year ago

I am realizing that this is issue is not clear enough I am closing it and will ask a more specific question