How to choose the appropriate gtf file?

Question

[pomodoro_sinensis]

Hello,

I think I may be overcomplicating things. I need to reproduce the data from a paper that uses the human hg19 (GRCh37) genome. When I have done the same with the most current human genome GRCh38, I just go to Ensembl (https://uswest.ensembl.org/Homo_sapiens/Info/Index ) and use those links to download the genome and the gtf file.

However, when I go to the Ensembl site for GRCh37 (http://grch37.ensembl.org/Homo_sapiens/Info/Index ), I am not able to find such a clear link for downloading the gtf. I have been googling around and I have found many gtf versions for that genome. I am getting a bit confused, could somebody help me where to find the "standard", or at least "equivalent" gtf file for GRCh37 as the one you can download from the link above for GRCh38?

Also any explanation on how to deal with different versions of genomes would be much appreciated. The paper only says GRCh37, but there seem to be many versions. How do you go about this sort of things?

Thanks so much!!

Answer 1

[GenoMax]

If you need hg19 versions then getting both the sequence and GTF file from GENCODE would be the best option.

[pomodoro_sinensis]

Thank you! That is real good advice.