Skip to content
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

Add 'genome' argument to makeTxDbFromGFF() #2

Open
hpages opened this issue Mar 23, 2024 · 0 comments
Open

Add 'genome' argument to makeTxDbFromGFF() #2

hpages opened this issue Mar 23, 2024 · 0 comments

Comments

@hpages
Copy link
Contributor

hpages commented Mar 23, 2024

Right now (as of txdbmaker 0.99.7) makeTxDbFromGFF() produces a TxDb object that has an unspecified genome by default. To change this, one needs to explicitely set the genome on the TxDb object returned by makeTxDbFromGFF(), e.g. with genome(txdb) <- "T2T-CHM13v2.0" (it's important to use the official name of the assembly otherwise the seqlevelsStyle() setter won't be able to switch the sequence naming style to UCSC or RefSeq). Alternatively one can specify the genome at creation time with makeTxDbFromGFF(..., metadata=data.frame(name="Genome", value="T2T-CHM13v2.0")) but this is admitedly poorly documented and not very convenient.

So let's add a genome argument to makeTxDbFromGFF().

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant