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,
Note the column Genome assembly version on the page to which you've linked. The last release for mm9 was Ensembl release 65, corresponding to GRCm37 / NCBIM37 / mm9. All subsequent releases were GRCm38 / mm10.
Edit: to be exact, the last annotation for mm9 is here: http://www.gencodegenes.org/mouse_releases/1.html