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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 quantify the reference transcripts #6

Open JXAUDZF opened 4 months ago

JXAUDZF commented 4 months ago

Hi，

I already have a reference transcript. How to quantify the existing reference transcripts and quantify the reference transcripts for each read sample

JXAUDZF

christopher-vollmers commented 4 months ago

Mandalorion doesn't quantify reference transcripts, only transcripts it identifies from the data. It also doesn't match the isoforms it identifies to reference transcripts because there are other tools that do that. For example gffcompare and SQANTI. You can use the Mandalorion quantification and use those tools to identify your transcripts of interest.

-Chris