[BioC] Error running makeTranscriptDbFromGFF in GenomicFeatures

Michael Lawrence lawrence.michael at gene.com
Thu Sep 4 13:56:40 CEST 2014


I think the error messages are a pretty good clue to what's wrong here. The
TxDb needs to know the "rank" (the order within the transcript) of each
exon. It tries to infer this from the positions, but this obviously fails
when exons within the same transcript fall on multiple chromosomes
(trans-splicing). When parsing the GTF, there is some problem with the
format. You could figure out the offending line(s) by cutting the file in
half recursively until the error goes away.

If you want, you could put the files up on dropbox, and I'll take a look at
them.

Michael



On Thu, Sep 4, 2014 at 3:23 AM, Jon Bråte <jon.brate at ibv.uio.no> wrote:

> Hi list,
>
> I am trying to create a TranscriptDb using GenomicFeatures, but I get an
> error message. I think there might be something wrong with my gff-file, but
> I am not sure. I also tried converting the gff-file to gtf, but also get an
> error.
>
> My goal with this is to plot the number of exons per gene.
>
> Code:
>
> #GFF-file
> > txdb = makeTranscriptDbFromGFF(file =
> "~/Documents/Prosjekter/RNA-project/Data/Sycon_ciliatum/sycon-from-Bergen/gff-files-and-expression-levels/cds.gb.gff3",
> + format = "gff")
> extracting transcript information
> Extracting gene IDs
> extracting transcript information
> Processing splicing information for gff3 file.
> Deducing exon rank from relative coordinates provided
> Warning message:
> In .deduceExonRankings(exs, format = "gff") :
>   Infering Exon Rankings.  If this is not what you expected, then please
> be sure that you have provided a valid attribute for exonRankAttributeName
> Error in unlist(mapply(.assignRankings, starts, strands)) :
>   error in evaluating the argument 'x' in selecting a method for function
> 'unlist': Error in (function (starts, strands)  :
>   Exon rank inference cannot accomodate trans-splicing.
>
> #GTF-file
> > txdbGTF = makeTranscriptDbFromGFF(file =
> "~/Documents/Prosjekter/RNA-project/Data/Sycon_ciliatum/sycon-from-Bergen/gff-files-and-expression-levels/cds.gb.gtf",
> + format = "gtf")
> Error in .parse_attrCol(attrCol, file, colnames) :
>   Some attributes do not conform to 'tag value' format
>
>
> > sessionInfo()
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
>  base
>
> other attached packages:
> [1] GenomicFeatures_1.16.2 AnnotationDbi_1.26.0   Biobase_2.24.0
>  GenomicRanges_1.16.3
> [5] GenomeInfoDb_1.0.2     IRanges_1.22.10        BiocGenerics_0.10.0
>
> loaded via a namespace (and not attached):
>  [1] BBmisc_1.7              BSgenome_1.32.0         BatchJobs_1.3
>    BiocParallel_0.6.1
>  [5] Biostrings_2.32.1       DBI_0.2-7
>  GenomicAlignments_1.0.5 RCurl_1.95-4.3
>  [9] RSQLite_0.11.4          Rcpp_0.11.2             Rsamtools_1.16.1
>   XML_3.98-1.1
> [13] XVector_0.4.0           biomaRt_2.20.0          bitops_1.0-6
>   brew_1.0-6
> [17] checkmate_1.3           codetools_0.2-9         digest_0.6.4
>   fail_1.2
> [21] foreach_1.4.2           iterators_1.0.7         rtracklayer_1.24.2
>   sendmailR_1.1-2
> [25] stats4_3.1.0            stringr_0.6.2           tools_3.1.0
>    zlibbioc_1.10.0
>
>
> ----------------------------------------------------------------
> Jon Bråte
>
> Section for Genetics and Evolutionary Biology (EVOGENE)
> Department of Biosciences
> University of Oslo
> P.B. 1066 Blindern
> N-0316, Norway
> Email: jon.brate at ibv.uio.no<mailto:jon.brate at ibv.uio.no>
> Phone: 922 44 582
> Web: mn.uio.no/ibv/english/people/aca/jonbra/index.html<
> http://mn.uio.no/ibv/english/people/aca/jonbra/index.html>
>
>
>
>
>
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