I have RNA-Seq data from a species A for which I don't have a reference genome. I would like to map this data on the closest available genome from species B.
I have read this post and I am planning to use
STAR. Does any of you have recommandations regarding the parameters to set for mapping, given that I don't have a reference genome? I would expect that I should use this program with less "stringency" than if I could map on the species A genome. For instance, the default parameter in
--outFilterMismatchNmax 10: should I set it to 20? 30? In
hisat2, it is
My reads are 100nt.
In addition, could you recommend any lecture related to this question?
Many thanks for your answers!