Hello,

I have a dataset of RNA bulk rna-seq (single-end), mapped with hisat2 and now I want to extract the sequences of some genes of my interest in order to run a Ka/Ks test for them I have one bam file for each sample! I am bit confused how to proceed, should I build a consensus alignment from all my bam files and then search for the genes of interest by coordinates or there is another way ?

Any help will be really appreciated