Differences when genome assembly changes in Kallisto

Question

[Mozart]

Hello everyone, I am running an experiment and trying to figure out why, when performing an RNA-seq experiment on an index made from two different versions of a mouse genome assembly, results are slightly different, in kallisto? In my specific case, for the same experiment I have 30 more genes differentially expressed with an older index compared to the newer one. I guess the newer versions are more curated then previous ones and this may resolve in more accurate (pseudo-)counts?

Thanks,

Answer 1

[igor]

an index made from two different versions of a mouse genome assembly, results are slightly different, in kallisto

Why should different versions of the genome have the same results? If there are different versions, there must be some differences.

30 genes out of at least 30,000 seems like a very minor difference.