Question: NCBI hg38 transcript annotation package GenomicFeatures
0
gravatar for zoe.ward
6 months ago by
zoe.ward0
zoe.ward0 wrote:

Hi all,

 

I'm very new to using GenomicFeatures and I'm trying to download a NCBI hg38 transcript annotation package (I want to use the built in functions such as promoters() etc).

Can someone direct me to where I can get this?

I have tried

> makeTxDbFromBiomart

but this isn't working for me and I get a timed out message (I'm not sure if this is actually the way to do it)

genomicfeatures • 144 views
ADD COMMENTlink modified 6 months ago by James W. MacDonald49k • written 6 months ago by zoe.ward0
Answer: NCBI hg38 transcript annotation package GenomicFeatures
0
gravatar for James W. MacDonald
6 months ago by
United States
James W. MacDonald49k wrote:
library(BiocInstaller)
biocLite("TxDb.Hsapiens.UCSC.hg38.knownGene")

If you use makeTxDbFromBiomart, you get a TxDb based on EBI/EMBL mappings, which is not the same as NCBI. UCSC is technically not the same either, but it is very close, and one could argue a bit cleaner.

ADD COMMENTlink written 6 months ago by James W. MacDonald49k
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