Once you download the GTF you can use https://agat.readthedocs.io/en/latest/tools/agat_sp_extract_attributes.html from AGAT toolkit to get the info.
Where to find all genes and their biotypes?
Hi all, I'm trying to figure out where I can get/make a file that contains gene names, their chromosome, position, their source, and their biotype. Like this:
chr start end gene biotype source
1 11869 14412 DDX11L1 pseudogene ensembl_havana
I'd like to get this for GRCh38 and GRCh37 - is there any resource that offers this or something similar that I can filter this information from?
I've tried searching ensembl and their FTP but I haven't found data that has this information in one place.
1 answer
This is all summarized in a GTF file, for example at https://www.ensembl.org/Homo_sapiens/Info/Index
Press "Download GTF", and then download the file. It contains exactly what you're asking for.
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