Closed quattro closed 2 years ago
Hey,
Great to hear that you find the package useful! Happy to implement a change on this, just to confirm is the issue that sex chromosomes are being pushed to lower chase e.g. X -> x. I believe you are right and that UCSC uses 'X' rather than 'x'.
Let me know if this is what you mean and I'll push a fix.
Cheers.
Hi @Al-Murphy , yes that's correct. I tested out my above suggestion and it appears to fix the issue for now.
Fix pushed to RELEASE_3_15 and will be available in Bioconductor in the next few days
Fantastic, thanks so much.
Hi all,
Thanks for the super cool tool. It's made my life a lot easier. I ran into a bug recently that took some internal messing around to figure out what was going on during
liftover
from GRCh37->GRCh38.Internally the code pushes all
CHR
to lowercase (see here), which in turn breaks the style requirements forUCSC
. It would be great to have this updated to work for all chromosome data, and not just autosomes.Perhaps instead of a blanket
tolower
call maybe use agsub
that explicitly replaces any'chr'
instance (regardless of case) with'chr'
.Cheers, Nick