Format restrictions for gtf files

[CodeCleanBICB]

Hello,

When calculating links with our scRNA, scATAC, and gtf file, we can only get links from peaks to gacc at the chromosome scaffold region, not the actual chromosomes. has this issue occurred to before?

We hypothesize that the problem occurred because there is an assumption about the chromosome format to be something like "chrm_12", instead of just "12". This may result in failure to read chromosome genes in the gtf dataframe, although the parsegtf package was able to load gtf file to dataframe just fine. Could you let us know which gtf file you used in your pipeline?

Thanks.