UCSC data anomaly in 50638 transcript(s): the cds cumulative length is
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@herve-pages-1542
Last seen 22 hours ago
Seattle, WA, United States
Hi Adi, Hope you don't mind that I'm cc'ing the list. On 05/27/2014 04:17 PM, Tarca, Adi wrote: > Dear Herv?, > > Should I worry about the warning below? > > I just want to overall some rna seq reads with know genes. Do you mean "overlap"? > > Thanks, > > Adi > > > txdb2=makeTranscriptDbFromUCSC( > > + genome="hg19", > > + tablename="knownGene") Note that we provide a few "TxDb" packages that contain pre-computed TranscriptDb objects for a few organisms and tracks: http://bioconductor.org/packages/release/BiocViews.html#___Transcri ptDb There is one for hg19/knownGene: the TxDb.Hsapiens.UCSC.hg19.knownGene package. > > Download the knownGene table ... OK > > Download the knownToLocusLink 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 TranscriptDb object ... OK > > Warning message: > > In .extractCdsLocsFromUCSCTxTable(ucsc_txtable, exon_locs) : > > UCSC data anomaly in 50638 transcript(s): the cds cumulative length is > > not a multiple of 3 for transcripts ???uc001aaa.3??? ???uc010nxr.1??? > > ???uc009vis.3??? ???uc009vjc.1??? ???uc009vjd.2??? ???uc009vit.3??? > ???uc009viu.3??? > > ???uc001aae.4??? ???uc001aai.1??? ???uc001aah.4??? ???uc009vir.3??? > ???uc009viq.3??? > > ???uc001aac.4??? ???uc009viv.2??? ???uc009viw.2??? ???uc009vix.2??? > ???uc009viy.2??? > > ???uc009viz.2??? ???uc010nxs.1??? ???uc009vje.2??? ???uc009vjf.2??? > ???uc009vjb.1??? > > ???uc001aak.3??? ???uc021oeg.2??? ???uc001aaq.2??? ???uc001aar.2??? > ???uc021oeh.1??? > > ???uc009vjk.2??? ???uc001aau.3??? ???uc001aax.1??? ???uc021oej.1??? > ???uc021oek.1??? > > ???uc021oel.1??? ???uc001abb.3??? ???uc001abe.4??? ???uc001abi.2??? > ???uc001abj.3??? > > ???uc009vjm.3??? ???uc010nxw.2??? ???uc001abl.3??? ???uc002khh.3??? > ???uc001abm.2??? > > ???uc001abo.3??? ???uc031pjj.1??? ???uc001abp.2??? ???uc021oem.2??? > ???uc009vjn.2??? > > ???uc009vjo.2??? ???uc031pjk.1??? ???uc001abt.4??? ???uc001abu.1??? > ???u [... truncated] This warning is wrong. It's actually easy to check that all the CDS have a cumulative length that is a multiple of 3: > cds_by_tx <- cdsBy(txdb2, by="tx") > table(sum(width(cds_by_tx)) %% 3L) 0 63691 Seems to be a regression introduced in BioC 2.14. Someone in Seattle will work on a fix and we will notify the list when the fix is available. Otherwise, assuming the code in charge of issuing the warning is working properly, you can get a legitimate warning like this for some combination of UCSC organism/track (but AFAIK never for the knownGene track). If all you want to do is find/count overlaps between some rna seq reads and known genes, then you probably don't care about CDS at all. Cheers, H. > > > sessioninfo() > > Error: could not find function "sessioninfo" > > > sessionInfo() > > R version 3.0.3 (2014-03-06) > > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > > [1] parallel stats graphics grDevices utils datasets methods > > [8] base > > other attached packages: > > [1] gplots_2.13.0 RColorBrewer_1.0-5 PADOG_1.4.0 > > [4] GSA_1.03 nlme_3.1-117 KEGGdzPathwaysGEO_1.1.3 > > [7] Heatplus_2.8.0 marray_1.40.0 limma_3.18.13 > > [10] org.Hs.eg.db_2.10.1 preprocessCore_1.24.0 GO.db_2.10.1 > > [13] SPIA_2.14.0 KEGGgraph_1.20.0 graph_1.40.1 > > [16] XML_3.98-1.1 KEGG.db_2.10.1 RSQLite_0.11.4 > > [19] DBI_0.2-7 R2HTML_2.2.1 rtracklayer_1.22.7 > > [22] Rsamtools_1.14.3 Biostrings_2.30.1 GenomicFeatures_1.14.5 > > [25] AnnotationDbi_1.24.0 Biobase_2.22.0 GenomicRanges_1.14.4 > > [28] XVector_0.2.0 IRanges_1.20.7 BiocGenerics_0.8.0 > > [31] BiocInstaller_1.12.1 multicore_0.2 > > loaded via a namespace (and not attached): > > [1] biomaRt_2.18.0 bitops_1.0-6 BSgenome_1.30.0 caTools_1.17 > > [5] gdata_2.13.3 grid_3.0.3 gtools_3.4.0 > KernSmooth_2.23-12 > > [9] lattice_0.20-29 RCurl_1.95-4.1 stats4_3.0.3 tools_3.0.3 > > *Adi Laurentiu TARCA, Ph.D.*** > > Assistant Professor (Research), > Department of Computer Science & Center for Molecular Medicine and > Genetics, Wayne State University, > Director, Bioinformatics and Computational Biology Unit, Perinatology > Research Branch (NICHD), > > 3990 John R., Office 4809, > Detroit, Michigan 48201 > Tel: 1-313-5775305 > -- 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 at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
Genetics GO Regression Cancer TranscriptDb Genetics GO Regression Cancer TranscriptDb • 2.2k views
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Tarca, Adi ▴ 570
@tarca-adi-1500
Last seen 11 months ago
United States
Dear Herv?, I have seen that type of error in google search but usually was for one or few transcripts. Seeing that the problem was for maybe all of the transcripts, I was not sure that the table was properly downloaded. Thank you for the clarification and for making others aware of the issue. Best regards, Adi -----Original Message----- From: Hervé Pagès [mailto:hpages@fhcrc.org] Sent: Wednesday, May 28, 2014 1:59 AM To: Tarca, Adi Cc: bioconductor at r-project.org Subject: Re: UCSC data anomaly in 50638 transcript(s): the cds cumulative length is Hi Adi, Hope you don't mind that I'm cc'ing the list. On 05/27/2014 04:17 PM, Tarca, Adi wrote: > Dear Herv?, > > Should I worry about the warning below? > > I just want to overall some rna seq reads with know genes. Do you mean "overlap"? > > Thanks, > > Adi > > > txdb2=makeTranscriptDbFromUCSC( > > + genome="hg19", > > + tablename="knownGene") Note that we provide a few "TxDb" packages that contain pre-computed TranscriptDb objects for a few organisms and tracks: http://bioconductor.org/packages/release/BiocViews.html#___Transcri ptDb There is one for hg19/knownGene: the TxDb.Hsapiens.UCSC.hg19.knownGene package. > > Download the knownGene table ... OK > > Download the knownToLocusLink 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 TranscriptDb object ... OK > > Warning message: > > In .extractCdsLocsFromUCSCTxTable(ucsc_txtable, exon_locs) : > > UCSC data anomaly in 50638 transcript(s): the cds cumulative length > is > > not a multiple of 3 for transcripts ......u [... truncated] This warning is wrong. It's actually easy to check that all the CDS have a cumulative length that is a multiple of 3: > cds_by_tx <- cdsBy(txdb2, by="tx") > table(sum(width(cds_by_tx)) %% 3L) 0 63691 Seems to be a regression introduced in BioC 2.14. Someone in Seattle will work on a fix and we will notify the list when the fix is available. Otherwise, assuming the code in charge of issuing the warning is working properly, you can get a legitimate warning like this for some combination of UCSC organism/track (but AFAIK never for the knownGene track). If all you want to do is find/count overlaps between some rna seq reads and known genes, then you probably don't care about CDS at all. Cheers, H.
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Hi Adi, This issue was being caused by some overly zealous warning code. It was throwing a warning whenever a CDS was absent (and not *only* when it was a non-viable length - as the warning says). I have fixed this so that the code is more reasonable about what it thinks you need to be warned about. Marc On 05/28/2014 08:52 AM, Tarca, Adi wrote: > Dear Herv?, > I have seen that type of error in google search but usually was for one or few transcripts. > Seeing that the problem was for maybe all of the transcripts, I was not sure that the table was properly downloaded. > Thank you for the clarification and for making others aware of the issue. > Best regards, > Adi > > -----Original Message----- > From: Hervé Pagès [mailto:hpages at fhcrc.org] > Sent: Wednesday, May 28, 2014 1:59 AM > To: Tarca, Adi > Cc: bioconductor at r-project.org > Subject: Re: UCSC data anomaly in 50638 transcript(s): the cds cumulative length is > > Hi Adi, > > Hope you don't mind that I'm cc'ing the list. > > On 05/27/2014 04:17 PM, Tarca, Adi wrote: >> Dear Herv?, >> >> Should I worry about the warning below? >> >> I just want to overall some rna seq reads with know genes. > Do you mean "overlap"? > >> Thanks, >> >> Adi >> >> > txdb2=makeTranscriptDbFromUCSC( >> >> + genome="hg19", >> >> + tablename="knownGene") > Note that we provide a few "TxDb" packages that contain pre-computed TranscriptDb objects for a few organisms and tracks: > > http://bioconductor.org/packages/release/BiocViews.html#___Trans criptDb > > There is one for hg19/knownGene: the TxDb.Hsapiens.UCSC.hg19.knownGene package. > >> Download the knownGene table ... OK >> >> Download the knownToLocusLink 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 TranscriptDb object ... OK >> >> Warning message: >> >> In .extractCdsLocsFromUCSCTxTable(ucsc_txtable, exon_locs) : >> >> UCSC data anomaly in 50638 transcript(s): the cds cumulative length >> is >> >> not a multiple of 3 for transcripts ......u [... truncated] > This warning is wrong. It's actually easy to check that all the CDS have a cumulative length that is a multiple of 3: > > > cds_by_tx <- cdsBy(txdb2, by="tx") > > table(sum(width(cds_by_tx)) %% 3L) > 0 > 63691 > > Seems to be a regression introduced in BioC 2.14. Someone in Seattle will work on a fix and we will notify the list when the fix is available. > > Otherwise, assuming the code in charge of issuing the warning is working properly, you can get a legitimate warning like this for some combination of UCSC organism/track (but AFAIK never for the knownGene track). If all you want to do is find/count overlaps between some rna seq reads and known genes, then you probably don't care about CDS at all. > > Cheers, > H. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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