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Xinglab / rmats-turbo

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output #176

Open zhangqc723 opened 2 years ago

zhangqc723 commented 2 years ago

I got some output using this tools,but,I can not find a gene that could be found in NCBI.Why?

EricKutschera commented 2 years ago

If your input --gtf has the gene and the gtf has isoforms which fit the alternative splicing definitions that rMATS uses (SE A5SS A3SS MXE RI) then you should see output for that gene in the fromGTF.[AS_Event].txt files. To get output for the gene in the [AS_Event].MATS.JC.txt files, your reads need to support the isoforms in the splicing event. If you ran with --b1 then you can check the aligned coordinates directly against the coordinates for that gene in the --gtf. If you ran with --s1 then you can check the bam files generated by rMATS in the --tmp directory