[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
Hervé Pagès
hpages at fhcrc.org
Tue Feb 7 21:37:28 CET 2012
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 at 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
>>>>
>>>
>>> _______________________________________________
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>>> Bioconductor at r-project.org
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>>> 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]]
>>
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>
>
--
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
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