makeTxDbFromUCSC fails to download refLink table
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@sebastien-vigneau-11153
Last seen 5.2 years ago
USA/Boston/Dana-Farber Cancer Institute

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!

genomicfeatures maketxdbfromucsc refseq • 1.6k views
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@herve-pages-1542
Last seen 1 day ago
Seattle, WA, United States

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.

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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.

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

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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.

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Great!

Thanks,

S.

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

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