I have several gtf-files and a gff3 file representing different sets of genes. I want to count the expression using HTSeq-count and input them all to DESeq2. But I am not sure what is the best approach. I was thinking that I could simply concatenate all the gtf and gff3 files, but some of the gtf-files have some overlapping gene names (with different isoforms), and the gff3-file will not be identical if I convert i to gtf. And if I count all the files separately, can I then concatenate the files later? What about the last few "special" lines produced by HTSeq if I use the HTSeq-import function in DESeq2?
I might also use Cuffdiff for comparison later, so I guess my question will also apply to Cuffdiff.