So I'm using an Ensembl gtf file (GrCh37) for rna-seq analysis and am wondering about the patches.
I know what the annotation patches are and why they're there, but should I exclude them when generating my count matrix in HTseq or Cufflinks? i.e. if I left them in, won't I get multi-reads mapping to both the patch and the original region, thereby screwing the true counts?
Thanks for your input, much appreciated.