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List:       bioc-devel
Subject:    Re: [Bioc-devel] Question: error in makeTxDbFromUCSC
From:       "Pages, Herve" <hpages () fredhutch ! org>
Date:       2019-01-29 4:11:46
Message-ID: 4254b3bd-4700-2715-9632-0203e46fa966 () fredhutch ! org
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Hi there,

I answered this yesterday on the support site:

    https://support.bioconductor.org/p/117265/#117346

Cheers,

H.

On 1/26/19 05:13, Vincent Carey wrote:
> If I am not mistaken the same problem is on the support site and I provided
> some
> commentary at https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconduc \
> tor.org_p_117265_-23117312&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJ \
> YbW0WYiZvSXAJJKaaPhzWA&m=XxwgvJX7-_q4u4p3uuJwItb8au40MB3h_gED2Ol9cXg&s=WKYBXF18xN-CQSEQtk0VghwXznKY3rcf94AR_IVcPfI&e=
>  
> 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@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
> > _______________________________________________
> > Bioc-devel@r-project.org mailing list
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo \
> > _bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSX \
> > AJJKaaPhzWA&m=XxwgvJX7-_q4u4p3uuJwItb8au40MB3h_gED2Ol9cXg&s=ZJNp-sK9VzvuJnoEM7n9rOkPECujgzbZHRsunathFnk&e=
> >  
-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages@fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

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