Hello , I am looking for mouse mm9 genome annotation file to use it in htseq count at the end. I decided to download it from gencode website(http://www.gencodegenes.org/mouse_releases/) On this website I downloaded m9 version. Does it correspond to ensembl mm9 build ? Actually at first I downloaded from UCSC table browser (http://genome.ucsc.edu/cgi-bin/hgTables?command=start) however I realized that in gtf file Transcript ID's and Gene ID's are same. So I think I ll use the gencode one if it is corresponding to mm9 build. Thanks,