RNA-seq analysis, wrong genome build

Question

[a_bis]

Hi, I have been doing a feature count and subsequent differential gene expression analysis on some RNA-seq samples which I now suspect is giving me poor results because I used a GRCm39 feature file from Ensembl but bam files which I suspect were aligned to mm10 (based on examination of bw files I produced from the bam files I was given from the sequencing facility).

Is there an Ensembl repository of feature files based on previous genome builds that I can access? I can't seem to find any on the Ensembl website! Alternatively, I believe I will have to re-align my fastq files to the new genome build, because as far as I can see, the Ensembl assembly converter tool doesn't support .bam files. Or is it 'safe' to just convert my gtf feature file from mm39 to mm10 using this Ensembl assembly converter, and then re-run the feature count? What would you do? Any input on how to best approach this will be much appreciated!

Answer 1

[Gregor Rot]

Hello, best would be to find the correct GTF at the Ensembl site, which has an archive of all releases up to 2009.

On the Ensembl mouse site (https://www.ensembl.org/Mus_musculus/Info/Index) simply click (bottom right) on "View in archive site" and choose the correct release.

Hope this helps.

[a_bis]

Thank you, that's really helpful!

Answer 2

[i.sudbery]

The ensembl archives keep copies of many of the old versions of ensembl. In this particular case, the last version of ensembl to be based on mouse GRCh38 was 102. The mouse download page for that can be accessed here: http://nov2020.archive.ensembl.org/info/data/ftp/index.html

[a_bis]

Thank you for the help!