RNAseq transcript quantification: how to deal with different number of genes in host organism?

Question

[Lina F]

Hi all,

I have RNAseq datasets from two organisms: one is the basic E. coli organism and the other one is the same E. coli, but I engineered it and added a gene. Now I would like to perform an RNAseq experiment and compare the differentially expressed genes.

I plan on quantifying the transcripts using sailfish. Should I map both organisms against the same reference transcript set (basic E. coli + that one gene) or is it more appropriate to map one dataset to just the basic E. coli transcript set and the other one to E. coli + added_gene?

Thanks for any advice!

Answer 1

[h.mon]

If you determined the exact insertion site of your gene, make a new reference with the gene inserted into the correct chromosomal position and map both onto this reference. Otherwise, use the E.coli + added_gene for both. No need to map on two "different" references.

[Lina F]

Thanks for the insight!