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Question: [Hinxton #251937] RE: GenomicFeatures::makeTranscriptDbFromBiomart - BioMart data anomaly: for some transcripts, the cds cumulative length inferred from the exon and UTR info doesn
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6.4 years ago by
Malcolm Cook1.5k
United States
Malcolm Cook1.5k wrote:
Dear Ensembl (genomes?) Help Can I please to get an update on where this issue stands? The last update I heard was from Karyn Megy, who wrote: I should be able to correct it for the next EnsemblGenome release (EG13, planned for mid/end-March), otherwise it'll be for EG14 (in May). Can I get a confirmation that Ensembl does indeed have the plan to address these data problems and whether the May timeframe is likely? Thanks! If there is anything I can do to assist further please advise..... ~Malcolm From: Rhoda Kinsella [mailto:rhoda@ebi.ac.uk] Sent: Monday, March 19, 2012 9:17 AM To: Hervé Pagès Cc: Cook, Malcolm; bioconductor@r-project.org Subject: Re: [Hinxton #251937] RE: [BioC] GenomicFeatures::makeTranscriptDbFromBiomart - BioMart data anomaly: for some transcripts, the cds cumulative length inferred from the exon and UTR info doesn't match the "cds_length" attribute from BioMart Hi Hervé and Malcolm, I have contacted the Ensembl genomes team who produce this database and have asked them to respond to you with an update. Regards Rhoda On 13 Mar 2012, at 20:31, Hervé Pagès wrote: Hi Malcolm, Rhoda, Did you hear back from the Ensembl helpdesk about this issue? AFAICT the issue is still in Ensembl release 66 (released 10 days ago). For example, when querying directly the Ensembl Mart, I get the following for transcript FBtr0079414 (dmelanogaster): Exon Rank in Transcript | Chromosome Name | Strand 1 | 2L | -1 2 | 2L | -1 Exon Chr Start (bp) | Exon Chr End (bp) 7218909 | 7220029 7218643 | 7218853 5' UTR Start | 5' UTR End | 3' UTR Start | 3' UTR End 7219112 | 7220029 | | | | 7218643 | 7218853 CDS Start | CDS End | CDS Length 1 | 203 | 204 204 | 204 | 204 Note that querying directly the Ensembl Mart thru the web interface allows me to choose database Ensembl Genes 66 but querying with the Bioconductor biomaRt package is still accessing Ensembl Genes 65, I wonder why, but this is a different story... So the "CDS Length" column (which, IIUC, is actually supposed to report the "Total CDS Length") is still incompatible with the exon/UTR starts and ends. If the exon/UTR starts and ends are correct then the total CDS length should be 203, not 204. But also, it could be that the exon/UTR starts and ends are incorrect. Finally note that there is no CDS region on exon 2 (the 3' UTR entirely spans exon 2) but the Ensembl Mart reports a CDS region of length 1 on this exon (CDS Start = CDS End = 204). This is probably why then the reported CDS Length is 204 (at least it's consistent with the highest "CDS End" value). Would be nice to see this dataset fixed. Thanks, H. On 02/15/2012 06:33 AM, Cook, Malcolm wrote: Dear helpdesk@ensemblgenomes.org<mailto:helpdesk@ensemblgenomes.org>, I am following up on this issue which I understand Rhoda Kinsella at EBI to have forwarded to you. I originally identified and reported the issue, first to the bioconductor email list where Rhoda picked up on it and replied as below. I am trying to ensure that there is a tracked issue with ensemblgenomes.org with my name on it - not that it has to be resolved with a fix, just I'd like to be assured I know as you resolve it. If there is anything further I can provide pertaining to describing or resolving the issue, please advise. Of course the issue may be in fact even further upstream - in flybase. I've not tried to find the root cause myself. Thanks, Malcolm Cook From: Rhoda Kinsella<rhoda@ebi.ac.uk<mailto:rhoda@ebi.ac.uk>> Date: Wed, 8 Feb 2012 10:27:02 -0600 To: Malcolm Cook<mec@stowers.org<mailto:mec@stowers.org>> Cc: Hervé Pagès<hpages@fhcrc.org<mailto:hpages@fhcrc.org>>, "bioconduc tor@r-project.org<mailto:bioconductor@r-project.org>"<bioconductor@r-p roject.org<mailto:bioconductor@r-project.org="">> Subject: Re: [Hinxton #251937] RE: [BioC] GenomicFeatures::makeTranscriptDbFromBiomart - BioMart data anomaly: for some transcripts, the cds cumulative length inferred from the exon and UTR info doesn't match the "cds_length" attribute from BioMart Hi Malcolm and Hervé This appears to be a data issue with the Drosophila core database which was then propagated into BioMart. I have forwarded the issue to the Ensembl Genomes project as they maintain this database and they will respond as soon as possible. Regards Rhoda On 7 Feb 2012, at 21:35, Cook, Malcolm wrote: Herve, Thanks so much for digging into this. Rhonda, I had submitted a ticket as suggested to Ensembl helpdesk, and have included them as recipients to this message (after changing the subject to include the issue tracker number). Ensembl helpdesk, I expect that Herve's detailed report, below, provides an example of the reported data anomaly that will help resolve the underlying issue. Cheers, ~Malcolm -----Original Message----- From: Hervé Pagès [mailto:hpages@fhcrc.org] Sent: Tuesday, February 07, 2012 2:37 PM To: Rhoda Kinsella; bioconductor@r-project.org<mailto:bioconductor@r-project.org> Cc: Cook, Malcolm Subject: Re: [BioC] GenomicFeatures::makeTranscriptDbFromBiomart - BioMart data anomaly: for some transcripts, the cds cumulative length inferred from the exon and UTR info doesn't match the "cds_length" attribute from BioMart Hi Rhoda, Malcolm, and others, So after taking a closer look at this, I can confirm that the reported "cds_length" looks wrong for some Fly transcripts. Take for example the FBtr0079414 transcript (minus strand): library(biomaRt) mart1<- useMart(biomart="ensembl", dataset="dmelanogaster_gene_ensembl") attributes<- c("ensembl_transcript_id", "strand", + "rank", "exon_chrom_start", "exon_chrom_end", + "5_utr_start", "5_utr_end", "3_utr_start", "3_utr_end", + "cds_length") filters<- "ensembl_transcript_id" values<- "FBtr0079414" getBM(attributes=attributes, filters=filters, values=values, mart=mart1) ensembl_transcript_id strand rank exon_chrom_start exon_chrom_end 5_utr_start 1 FBtr0079414 -1 1 7218909 7220029 7219112 2 FBtr0079414 -1 2 7218643 7218853 NA 5_utr_end 3_utr_start 3_utr_end cds_length 1 7220029 NA NA 204 2 NA 7218643 7218853 204 2 exons: The 3' UTR (located on exon 2) spans the entire exon so no CDS on this exon. The start of the 5' UTR (located on exon 1) is 203 bases upstream of the exon start. But the reported cds_length is 204. Something looks wrong. For other transcripts, e.g. FBtr0300689 (plus strand), things look OK: getBM(attributes=attributes, filters=filters, values=values, mart=mart1) ensembl_transcript_id strand rank exon_chrom_start exon_chrom_end 5_utr_start 1 FBtr0300689 1 1 7529 8116 7529 2 FBtr0300689 1 2 8193 9484 NA 5_utr_end 3_utr_start 3_utr_end cds_length 1 7679 NA NA 855 2 NA 8611 9484 855 2 exons: The end of the 5' UTR (located on exon 1) is 437 bases upstream of the exon end. The start of the 3' UTR (located on exon 2) is 418 bases downstream of the exon start. So the CDS total length is 437 + 418 = 855, as reported. @Malcolm and other makeTranscriptDbFromBiomart() users: I'm about to commit a patch to this function so that this anomaly in the Ensembl data causes a warning instead of an error. Also the warning will display the first 6 affected transcripts. The patch will make it into GenomicFeatures 1.6.8 (release) and 1.7.14 (devel), which will become available via biocLite() in the next 24-36 hours. Cheers, H. On 02/06/2012 02:18 PM, Hervé Pagès wrote: Hi Rhoda and others, I still need to check that this error issued by internal helper .extractCdsRangesFromBiomartTable() about "the cds cumulative length inferred from the exon and UTR not matching the cds_length attribute from BioMart" is not a FALSE positive. I'm planning to patch the code in charge of this sanity check so it issues a warning instead of an error and it displays something more useful than just "for some transcripts etc...". Would be nice to know at least for which transcript. I'll keep you informed, thanks! H. On 02/06/2012 12:53 AM, Rhoda Kinsella wrote: Hi Malcolm and Marc, Please submit an Ensembl helpdesk ticket about this issue along with a detailed example to (helpdesk@ensembl.org<mailto:helpdesk@ensembl.org>) and we will look into it. Kind regards Rhoda On 3 Feb 2012, at 20:32, Cook, Malcolm wrote: Hi Marc, and other library(GenomicFeatures) users working in fly, I just changed Subject to keep alive one of the issues I still have, namely: I get the following error: library(GenomicFeatures) txdb<-makeTranscriptDbFromBiomart(biomart="ensembl", dataset="dmelanogaster_gene_ensembl", circ_seqs=NULL)) Download and preprocess the 'transcripts' data frame ... OK Download and preprocess the 'chrominfo' data frame ... OK Download and preprocess the 'splicings' data frame ... Error in .extractCdsRangesFromBiomartTable(bm_table) : BioMart data anomaly: for some transcripts, the cds cumulative length inferred from the exon and UTR info doesn't match the "cds_length" attribute from BioMart Marc, you already observed that: the data for cds ranges and total cds length (both from biomaRt) no longer agree with each other. In other words, the data from the current drosophila ranges in biomaRt seems to disagree with itself, and so the code is refusing to make a package out of this data as a result. To get the 2nd issue fixed probably involves talking to ensembl about their CDS data for fly to see if we can resolve the discrepancy. I would be happy to take this to them. I still wonder: Can you recommend a best way to get a more diagnostic trace from the attempt at txdb creation so we can correctly report to ensembl team the errant transcript(s) ? I would be happy to take this up with Ensembl team, but, need details which I don't know how to produce. Finally, one the side, here is a tiny suggestion: * change the default for circ_seqs in makeTranscriptDbFromBiomart to be NULL, instead of any organism (human) specific. Regards, --Malcolm R version 2.14.0 (2011-10-31) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicFeatures_1.6.7 AnnotationDbi_1.16.11 Biobase_2.14.0 [4] GenomicRanges_1.6.6 IRanges_1.12.5 loaded via a namespace (and not attached): [1] BSgenome_1.22.0 Biostrings_2.22.0 DBI_0.2-5 RCurl_1.9-5 [5] RSQLite_0.11.1 XML_3.9-4 biomaRt_2.10.0 rtracklayer_1.14.4 [9] tools_2.14.0 zlibbioc_1.0.0 _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org<mailto:bioconductor@r-project.org> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Rhoda Kinsella Ph.D. Ensembl Production Project Leader, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK. [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org<mailto:bioconductor@r-project.org> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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@fhcrc.org<mailto:hpages@fhcrc.org> Phone: (206) 667-5791 Fax: (206) 667-1319 Rhoda Kinsella Ph.D. Ensembl Production Project Leader, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK. -- 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@fhcrc.org<mailto:hpages@fhcrc.org> Phone: (206) 667-5791 Fax: (206) 667-1319 Rhoda Kinsella Ph.D. Ensembl Production Project Leader, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK. [[alternative HTML version deleted]]