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Question: makeTxDbFromUCSC fails to download refLink table
1
gravatar for Sebastien Vigneau
16 months ago by
USA/Boston/Dana-Farber Cancer Institute
Sebastien Vigneau10 wrote:

The following command fails with the message below, using R version 3.3.1 and Bioconductor version 3.3 on Ubuntu 16.04:

> txdb <- makeTxDbFromUCSC(genome = 'mm10', tablename = "refGene")
Download the refGene table ... OK
Download the refLink table ... Error in normArgTable(value, x) : unknown table name 'refLink'

Do you know what the problem might be and how to solve it?

Thank you for your help!

ADD COMMENTlink modified 16 months ago by Hervé Pagès ♦♦ 13k • written 16 months ago by Sebastien Vigneau10
3
gravatar for Hervé Pagès
16 months ago by
Hervé Pagès ♦♦ 13k
United States
Hervé Pagès ♦♦ 13k wrote:

Hi Sebastien,

An easier way to reproduce is with:

library(rtracklayer)
session <- browserSession()
genome(session) <- "mm10"
query <- ucscTableQuery(session, table="refLink")
# Error in normArgTable(value, x) : unknown table name 'refLink'

This worked until very recently. So something must have changed at UCSC that breaks it. And indeed (after browsing around a bit):

http://genome.ucsc.edu/FAQ/FAQdownloads.html#download35

In short, the refLink table has changed location and is now in a separate (shared across organisms) db. However, for whatever reason, I don't seem to be able to access the table at its new location (using its fully qualified name) with rtracklayer:

> query <- ucscTableQuery(session, table="hgFixed.refLink")
Error in normArgTable(value, x) : unknown table name 'hgFixed.refLink'

So we will need assistance from Michael, our rtracklayer expert, before we can come up with a fix for makeTxDbFromUCSC().

Thanks for reporting this. We'll keep you posted here about any progress on this.

H.

ADD COMMENTlink modified 16 months ago • written 16 months ago by Hervé Pagès ♦♦ 13k
1

For some reason the table browser does not report hgFixed.refLink when selecting "All Tables" for the group. Seems like a bug in the table browser to me. I guess we should bring it up with UCSC.

ADD REPLYlink written 16 months ago by Michael Lawrence9.8k

Thank you for looking into this. I am looking forward to Michael's feedback.

ADD REPLYlink written 16 months ago by Sebastien Vigneau10
1

Hi Sebastien,

This is fixed in GenomicFeatures 1.24.5 (release) and 1.25.16 (devel). Both versions should become available via biocLite() in the next 48 hours or so (maybe a little bit more for the devel version).

Cheers,

H.

ADD REPLYlink written 16 months ago by Hervé Pagès ♦♦ 13k

Great!

Thanks,

S.

ADD REPLYlink written 16 months ago by Sebastien Vigneau10

I still have this problem in R 3.3.2. bioconductor 3.4. and rstacklayer 1.34.1

Is there any solution for me? Thank you!

> library(rtracklayer)
> session <- browserSession()
> genome(session) <- "hg19"
> query <- ucscTableQuery(session, table="refLink")
Error in normArgTable(value, x) : unknown table name 'refLink'
ADD REPLYlink written 9 months ago by jockbanan0

As stated in the post above, the table is now called "hgFixed.refLink".

ADD REPLYlink written 9 months ago by Michael Lawrence9.8k
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