[Bioc-devel] Question: error in makeTxDbFromUCSC

[Pages, Herve]

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.bioconductor.org_p_117265_-23117312&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&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 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
>> _______________________________________________
>> Bioc-devel using 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_wJYbW0WYiZvSXAJJKaaPhzWA&m=XxwgvJX7-_q4u4p3uuJwItb8au40MB3h_gED2Ol9cXg&s=ZJNp-sK9VzvuJnoEM7n9rOkPECujgzbZHRsunathFnk&e=
>>
-- 
Hervé Pagès

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