mm9 gtf file gencode

Question

[skylinesky]

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,

Answer 1

[Kevin Blighe]

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 (see below)

[lr65358]

Here's the current version of the link: https://www.gencodegenes.org/mouse/release_M1.html

[Kevin Blighe]

Thank you. The link that I originally posted has expired.