This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Pool male and female individuals for de novo transcriptome assembly?

Hi, I have what I think is a simple question:

Is it appropriate to combine reads from males and females for de novo transcriptome assembly?

I have an RNAseq dataset consisting of 8 females and 21 males, I've done a de novo assembly on a single individual as a first pass and it looks pretty good, but it makes sense to leverage the amount of data I have for a more complete transcriptome. Is there any potential issue with combining both sexes?

Thanks!

rna-seq assembly
• 1,406 views • link
updated by WouterDeCoster WouterDeCoster • written by nsimons • nsimons

1 answer

Well, apart from sex chromosomes and gender-specific expression on those, I don't think there is a reason not to combine all your data.

As a sanity check, you could also assemble all males and compare that to the assembly of all animals.

• 0 views • link
written by WouterDeCoster WouterDeCoster

Log in to answer this question.

More posts like this