Jack Humphrey
Jack Humphrey
hi, sorry for the delay. Which version of regtools are you using?
If you read the error message it clearly says you don't have the optparse R package installed.
In an R session run library(optparse). If it gives an error then you need to install it with install.packages("optparse")
@davidaknowles can you look into this?
Sorry for the delay. Hi, I believe the intronMotif option will keep novel junctions, as long as they have a defined strand. So yes this would remove non-canonical unannotated junctions,...
You're providing a single junction file as the -j argument. It should instead be a file containing a list of paths to junction files.
yes this is a known issue. This is due to GTF and BED file formats having different specifications for genomic intervals being either 0-based or 1-based - I can never...
Yes this is a known issue, I've proposed a fix for it - waiting for @davidaknowles to approve: https://github.com/davidaknowles/leafcutter/pull/162 In the meantime you can grep -v "?" your junction files...
Hi both, If you're sure there are no "?" in the junction files, did you try using the --checkchrom flag?
Hi @Tommeri, what chromosome names are present in your junction file? I believe that --checkchrom only works if you have chr1 or 1 style chromosome names. I've proposed a fix...