I am using ChIPseeker, however when I open the annotation source file such as Mus_GRCm38_94.gtf, it tells me that is unavailable. However, I was able to see the content of the file. 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.
Thank you.
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:
Thanks!
Thank you. Do you happen to know how to remove header line? The file is too big to do it manually.
Thank you,
Sorry @yaklich1904, I missed replying sooner! Hopefully, you found the method already but if not…
Instructions are in the linked post I sent before but are also here in our FAQs.
https://galaxyproject.org/support/