Plot exon number per gene and transcript lengths
0
Entering edit mode
Jon Bråte • 180
@jon-brate-6263
Last seen 25 days ago
Norway
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/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. 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 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=""> [[alternative HTML version deleted]]
Genetics TranscriptDb GenomicFeatures • 1.3k views
ADD COMMENTlink

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 217 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.4