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christopher-vollmers / Mandalorion

Pipeline to identify isoforms from full-length cDNA sequencing data
MIT License
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how to get the gene id of transcript #5

Open JXAUDZF opened 6 months ago

JXAUDZF commented 6 months ago

the Isoform clean gtf file has not gene id and transcript id, therefore how to acquire the gene id of specific trancript?

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christopher-vollmers commented 6 months ago

The newest version on Mandalorion (4.5) actually adds a meaningful gene_id. You'd just have to update and run it again with "-M FQ" (without the quotations). Should be very fast.

transcript_id are harder. I recommend you use Sqanti3 for that, which will match your isoforms to the annotation and give you a bunch of extra information as well.