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Bioconductor / GenomicFeatures

Query the gene models of a given organism/assembly
https://bioconductor.org/packages/GenomicFeatures
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Add 'genome' argument to makeTxDbFromGFF() #55

Closed hpages closed 7 months ago

hpages commented 1 year ago

Edit: All makeTxDb*() functions have moved to the new txdbmaker package. So I re-created this issue there and I'm closing this one.

Right now (as of GenomicFeatures 1.51.4) 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().

PanZiwei commented 11 months ago

Hi, I am interested to use genomic annotation for T2T. Does Genomicfeatures support the T2T loading? If so, can you provde more hints on that? Thank you!

> makeTxDbFromGFF(..., metadata=data.frame(name="Genome", value="T2T-CHM13v2.0"))
Error: '...' used in an incorrect context
hpages commented 11 months ago

Your question is barely related to this issue. I opened a separate issue where I answer your question. See issue #65. Please use that other issue for any follow-up. Thanks!

H.

hpages commented 7 months ago

All makeTxDb*() functions have moved to the new txdbmaker package. So I re-created this issue there and I'm closing this one.