Mapping to transcriptome without gtf annotation
Hi!
Would it be okay to perform mapping of RNA seq reads to a transcriptome assembly without using a gtf file? I am using STAR.
Thanks!
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Michael Dondrup
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ZuelTech •
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ZuelTech •
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Use
salmoninstead of STAR. Easy to use. Will allow multimapping reads to be accounted for properly. Significantly less compute resources required. Get started: https://salmon.readthedocs.io/en/latest/.Thanks! Would it be okay to perform mapping (using any mapping tools) without gtf annotation?
It depends on what you mean by "okay" and what you want to do with the results after that. Sequence alignment is (obviously) going to work. You would need a GTF file for generating gene counts if you had a genome, but you don't have that. Therefore, I would follow GenoMax's recommendation; it is "the okay" way.