[BioC] [Hinxton #251937] RE: 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

Cook, Malcolm MEC at stowers.org
Wed Feb 15 15:33:31 CET 2012


Dear helpdesk at 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 at ebi.ac.uk<mailto:rhoda at ebi.ac.uk>>
Date: Wed, 8 Feb 2012 10:27:02 -0600
To: Malcolm Cook <mec at stowers.org<mailto:mec at stowers.org>>
Cc: Hervé Pagès <hpages at fhcrc.org<mailto:hpages at fhcrc.org>>, "bioconductor at r-project.org<mailto:bioconductor at r-project.org>" <bioconductor at r-project.org<mailto:bioconductor at 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 at fhcrc.org]
Sent: Tuesday, February 07, 2012 2:37 PM
To: Rhoda Kinsella; bioconductor at r-project.org<mailto:bioconductor at 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 at ensembl.org<mailto: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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Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.


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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<mailto:hpages at 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.



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