vicasze
commented
1 year ago ok, I found it myself, sorry to have bothered.
It can be found from the UCSC Browser --> Tools --> Table Browser. The refGene.txt has the right format, and step 4. Build refgene_anno works.
However, step 5. "Build the feat_annotation asset" doesn't work because the asset ensemb_rb has not been created. In the documentation, there is no step explaining how to create this asset. (maybe this needs to be added?)
Anyway, I think in my case this won't be possible, as I could not find a regulatory build file analogous to the human (https://ftp.ensembl.org/pub/release-108/regulation/homo_sapiens/). I guess I won't be able to run the pipeline to full potential, but it will still work, so that's ok.
Thank you (I guess the issue can be closed).
Hi, Thank you for a great tool.
I would like to use peppro in pig samples (ss11 - sus scrofa 11). I am following the documentation "custom reference data" to build the assets, as refgenie does not have them already. However, I am stuck at the step 4 . Build refgene_anno, probably because I don't seem to find the necessary refGene.txt file.
I have so far tried to use the refGene.gtf and the ensGene.gtf from https://hgdownload.soe.ucsc.edu/goldenPath/susScr11/bigZips/genes/ , but it is a gtf, not a .txt file, and does not have the same format as your human refGene.txt.
Could you point to the right type of file I should be using?
Thank you