-
Notifications
You must be signed in to change notification settings - Fork 126
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
ERROR Found in .fastTSSCounts for creating arrowfile #2127
Comments
Hi @macrophage666! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other |
have you solved it? I met the same error |
Here are some tutorials for helping you forge your customized BSgenome and Txdb package: It might take some time to get those two packages ready, but there is a high chance that your problems will be solved by doing so. I would like to help if you meet other problems in this process. |
Thank you very much. I have built the BSgenome and Txdb packages, but I'm still encountering the same error. What confuses me is what you mentioned about excluding the unknown chromosomes. What do you mean by "unknown chromosomes"? |
And I have posted an issue at https://github.com/GreenleafLab/ArchR/issues/2149#issue-2246455525 |
Thanks for providing your original post. Your case is more complicated. I found that the genome for the organism you used only had one assembled chromosome: the chr for mitochondria. The others are just the scaffolds. In my case, only a few genes were at the scaffold level, so I just excluded those scaffolds in the genome annotation, and it works. You could not do that since most of your genes are in scaffold level. You can try just keep that assembled chromosome for creating arrowfile which probably will work. This post discussed why the scaffold might not work: #88 (comment) |
Hi,
I have trouble creating an arrowfile. I have non-standard chromosomes for our fragment files, so I customized the geneAnnotation and genomeAnnotation which have the same seqnames with our fragment files but I still got this error. Here is log:
ArchR-createArrows-2d96605e219c6f-Date-2024-03-04_Time-14-05-54.045259.log
Thanks
The text was updated successfully, but these errors were encountered: