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qqwang-berkeley / JUM

A tool for annotation-free differential analysis of tissue-specific pre-mRNA alternative splicing patterns
MIT License
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Regarding Error "NONE" after running JUM_C.sh #48

Closed heebaanjum closed 1 year ago

heebaanjum commented 1 year ago

Hello everyone,

After running JUM_C.sh, the output files from FINAL_JUM_OUTPUT_pvalue_0.05, have all the identified events as "NONE". Not even single event is annotated to transcript_id. Please help me to figure out what exactly is the error, because atleast some of the events should be annotated to a gene or transcript id.

I have attached below first 10 lines of genePred file used for --REF argument. MSU_v7_genepred_first_10_lines.txt

Could you please help me to troubleshoot this? Thank you so much

qqwang-berkeley commented 1 year ago

Your gene annotation format is wrong. Please make sure that it is compatible with the refFlat file format. Something like: ZNF639 NM_001375803 chr3 + 179323030 179338583 179328293 179334422 5 179323030,179328282,179329617,179332988,179333268, 179323291,179328351,179329728,179333123,179338583, WASH7P NR_024540 chr1 - 14361 29370 29370 29370 11 14361,14969,15795,16606,16857,17232,17605,17914,18267,24737,29320, 14829,15038,15947,16765,17055,17368,17742,18061,18366,24891,29370, MIR6859-1 NR_106918 chr1 - 17368 17436 17436 17436 1 17368, 17436, MIR6859-2 NR_107062 chr1 - 17368 17436 17436 17436 1 17368, 17436,