Question: RNA-seq analysis of two species
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afli • 190 wrote:
Dear all,
I have RNA-seq samples of two related species with similar genomes. The quality of genomes are good, is there any ways to map and compare the differential genes between them?
As far as I know, kallisto can calculate expression levels for each transcripts in each species, but this would require me to do some blat jobs to find the homologous genes between these two species and then do comparation. I just wonder if there is any other better ways? Thank you!
Aifu.
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modified 2.3 years ago
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Charles Warden ♦ 8.0k
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2.3 years ago by
afli • 190
Hi, Similar question here
Thank you. I see the post, in your case, you have one genome that is of low quality. This is different from mine, the two genome are both of high quality, and they are similar. If I align the two sample reads to one reference genome, the reference genome itself is some different from the two genome. Is is possible to do something more precisely?
I am not an expert, I don't want to tell you a wrong answer, but in your case maybe I would check the genomes similarity by mapping reads from species 2 to species 1 (or/and species 1 to species 2) and see the overall alignment rate. And if it is good enough for what you want to do, use this genome as a reference (this is still a non expert opinion).
OK, thank you for your advice.
Depending on what species you're working on, you could find ortholog information in ensembl. I think that would be a much better approach than mapping the RNA-seq of the two species to the genome of one of them.
All right, thank you~