[Bioc-devel] Question: error in makeTxDbFromUCSC
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 ??? < chen.shihang at 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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