I am new to Bioinformatics and I am exploring the refGene.txt files from the UCSC genome annotation database for several species.

My question concerns the Dec. 2011 (GRCm38/mm10) assembly of the mouse genome. I have seen that the Human one (hg39) contains both coding and non-coding transcripts. But the Mouse (mm10) RefGene.txt only contains coding transcripts.

Why is that?

Source of the file: http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/refGene.txt.gz

  • $\begingroup$ Is there a reason you're using refseq rather than the more complete annotations from Ensembl/Gencode? $\endgroup$ – Devon Ryan Apr 2 '19 at 11:31
  • $\begingroup$ Yes, it is an exercise in a course. I am to use bash shell and gawk to extract some information from several refGene.txt files. The question about the absence of non-coding transcripts in mouse is not part of the exercise, but have puzzled me. I have been looking for info about it, but I haven't a clear explanation. $\endgroup$ – jorvaor Apr 2 '19 at 12:02

It wasn't the correct file. I downloaded the file again from UCSC, compared it with the file that I was using, and they were different. This new file contained both information from coding and non-coding transcripts.

To all the kind people that took interest in my problem, I am sorry.

Edited 30/12/2020: To add a bit of clarity; the link in the question is the correct link from which to download the correct file. The file with which I was working from the beginning was the wrong one, but I don't really know where I got it from the first time.


Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.