Mapping to transcriptome without gtf annotation
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10 weeks ago
ZuelTech • 0

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!

transcriptome Mapping assembly • 367 views
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Use salmon instead 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/.

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Thanks! Would it be okay to perform mapping (using any mapping tools) without gtf annotation?

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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.

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