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().
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 bymakeTxDbFromGFF(), e.g. withgenome(txdb) <- "T2T-CHM13v2.0"(it's important to use the official name of the assembly otherwise theseqlevelsStyle()setter won't be able to switch the sequence naming style to UCSC or RefSeq). Alternatively one can specify the genome at creation time withmakeTxDbFromGFF(..., metadata=data.frame(name="Genome", value="T2T-CHM13v2.0"))but this is admitedly poorly documented and not very convenient.So let's add a
genomeargument tomakeTxDbFromGFF().