[BioC] Error running makeTranscriptDbFromGFF in GenomicFeatures

[Jon Bråte]

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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