Format help for GTF datasets

[jennaj]

@yaklich1904

I also have a link such as ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M18/gencode.vM18.annotation.gtf.gz. I used to able to open and use it and now ChIPseeker tells me it is unavailable. I am wondering what could be the problem.

GTF datasets from this source include header lines which make the data out of specification for the type. The datatype GFF is probably currently assigned. Remove the header lines and reassign the GTF datatype. How-to is covered in this prior Q&A:

No Reference GFF file available in ClosestBed tool

Hi, I was trying to match my ChIP-seq peaks with nearest genes, for what I thought I’d use the ClosestBed tool. However there are no built-in GFF files available. Could you please add one for mouse? [14] Many thanks!

Thanks!