I have a set of files derived from a WGS experiment. Using Qualimap, I found a mean coverage of about 30x, which was expected.
I now need to concentrate on a single gene, so I aligned these files against the reference for that gene instead that all the human genome. Now the coverage is about 1000x. Something is not right.
So, my question is: what is the best practice to align for a specific reference? Shall I align the fastq files against the reference of the gene of interest (as I have done now)? Or against the whole human genome (since the main experiment was on human WGS) and extract from there?