[Bioc-devel] Question: error in makeTxDbFromUCSC

Vincent Carey @tvjc @end|ng |rom ch@nn|ng@h@rv@rd@edu
Sat Jan 26 14:13:43 CET 2019

If I am not mistaken the same problem is on the support site and I provided
commentary at https://support.bioconductor.org/p/117265/#117312

Let's keep the discussion there.  The "problem" seems to be upstream at
UCSC.  There
may be a design approach that avoids the risk of asynchrony between
separate resources
and community input can be useful on this.

On Fri, Jan 25, 2019 at 10:42 PM 陈施航 <
chen.shihang using genome.rcast.u-tokyo.ac.jp> wrote:

> Hi GenomicFeatures support,
> I am Shihang Chen, a phD student at the University of Tokyo, using
> GenomicFeatures for ChIPSeeker.
> I run into a problem when I was using makeTxDbFromUCSC, and really need
> your help.
> After I run
> txdb=makeTxDbFromUCSC(genome="hg19",tablename="refGene")
> I got this error.
> Download the refGene table ... OK
> Download the hgFixed.refLink table ... OK
> Extract the 'transcripts' data frame ... OK
> Extract the 'splicings' data frame ... OK
> Download and preprocess the 'chrominfo' data frame ... OK
> Prepare the 'metadata' data frame ... OK
> *Make the TxDb object ... Error in .check_foreign_key(transcripts_tx_chrom,
> NA, "transcripts$tx_chrom",  : *
> *  all the values in 'transcripts$tx_chrom' must be present in
> 'chrominfo$chrom'*
> I consider the problem is that refGene version was upgraded last
> November,however, GenomicFeatures haven't done corresponding changes to the
> new refGene release.
> I attached my survey report in this email.
> If you have any clues why this is happening, please let me know.
> Your help is much appreciated.
> Thank you so much!
> Shihang Chen
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