Hi, I like to use the ChIPseeker to annotate my ChIP-seq result.
My reference genome is hg19.
Although I’ve tried to download it from the UCSC website, none of the downloaded files can get the analysis work.
I don’t know if my GFT file is not right for the tool.
Does anyone know where I can download the GTF file for my analysis?
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Hey, how did you solve this problem. I don’t have available built-in GFT files as well. Don’t know how to do the annotation.
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There is much Q&A at this site about how to obtain and format a GTF properly for use with tools. I added some tags to this post to help find it.
This FAQ may also help. It has a focus on DE analysis, but the reference annotation advice applies to any tool that accepts a GTF input.