Mapping to transcriptome without gtf annotation

Question

[Biodee]

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!

[GenoMax]

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/.

[Biodee]

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

[Michael]

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.