Finding equivalence between annotations from different species
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9 weeks ago
zhtsandres • 0

I have used Hisat2 to map some RNAseq reads against a brand-new genome assembly from the same species. In the literature the same reads were mapped against the reference genome of a different species of the same genus (because, despite the differences, this reference genome is more complete and better annotated). As expected, the alignment rates were around 10-15% higher when mapped to the same species. However, since this genome is brand new there is no annotation available yet, so I used StringTie to make myself a basic annotation for gene count and Differential Expression Analysis.

Is there any way to know which gene ids between both reference and self-made annotations match to the same RNA reads, and then identify gene ids that are present in one but not the other?

Thanks

Genome RNAseq Stringtie Annotation • 117 views
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Entering edit mode
9 weeks ago
icemduru ▴ 20

maybe https://github.com/agshumate/Liftoff might be useful

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