Plot exon number per gene and transcript lengths
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Jon Bråte • 180
Last seen 25 days ago
Hi, I want to create plots like the number of exons per gene in a list of genes, and the lengt of transcripts. My first choice would be to use R/Bioconductor and gtf/gff files, but I haven't found any good ways of doing this. I tried using GenomicFeatures and make a TranscriptDB but I get the following error on my gff file: > txdb = makeTranscriptDbFromGFF("~/Documents/Prosjekter/RNA- project/Data/Sycon_ciliatum/sycon-from-Bergen/gff-files-and- expression-levels/", + 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. Appreaciate any suggestions! > 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 Br?te Section for Genetics and Evolutionary Biology (EVOGENE) Department of Biosciences University of Oslo P.B. 1066 Blindern N-0316, Norway Email: jon.brate at<mailto:jon.brate at=""""> Phone: 922 44 582 Web:<http: mn.uio.="" no="" ibv="" english="" people="" aca="" jonbra="" index.html=""> [[alternative HTML version deleted]]
Genetics TranscriptDb GenomicFeatures • 1.3k views

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