Question: mm9 gtf file gencode
1
gravatar for skylinesky
2.4 years ago by
skylinesky10
skylinesky10 wrote:

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,

rna-seq htseq count mm9 gtf • 3.1k views
ADD COMMENTlink modified 2.4 years ago by Kevin Blighe60k • written 2.4 years ago by skylinesky10
0
gravatar for Kevin Blighe
2.4 years ago by
Kevin Blighe60k
Kevin Blighe60k wrote:

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)

ADD COMMENTlink modified 6 months ago • written 2.4 years ago by Kevin Blighe60k
1

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

ADD REPLYlink written 6 months ago by lr6535820

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

ADD REPLYlink written 6 months ago by Kevin Blighe60k
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