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  • Annotation for S. pombe in GAGE.

    I am trying this workflow: "RNA-Seq Data Pathway and Gene-set Analysis Workflows
    Weijun Luo" but on S. pombe and not human data.
    In part 3.2 it starts with:

    > library(TxDb.Hsapiens.UCSC.hg19.knownGene)

    I need help with finding the corresponding package for S. pombe!

    Please help!
    /Parham

  • #2
    You would need to construct your own TranscriptDb object using function like makeTranscriptDbFromGFF from the GenomicFeatures package:
    library(GenomicFeatures)
    ?makeTranscriptDbFromGFF

    You may download the GFF data for S. pombe genome from:
    PomBase is a comprehensive database for the fission yeast Schizosaccharomyces pombe, providing structural and functional annotation, literature curation and access to large-scale data sets

    I haven’t go through the whole process, but it should work theoretically.

    In addition, makeTranscriptDbFromUCSC and makeTranscriptDbFromBiomart in GenomicFeatures package are more staightfoward for species with genome annotation in UCSC or Biomart database. UCSC does not have annotation data for S. pombe genome. You may try makeTranscriptDbFromBiomart if you confirmed Biomart has the data.
    More details on GenomicFeatures package:
    A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources will be supported in the future). This information is then stored in a local database that keeps track of the relationship between transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format.

    Comment


    • #3
      Thanks for the tips bigmw, I will give it a try and see how it will goes.

      Cheers,
      /P

      Comment


      • #4
        makeTranscriptDbFromBiomart for S. pombe

        I just posted an approach to using Biomart at https://www.biostars.org/p/103251/

        Here's the nub:

        Code:
        txdb<-makeTranscriptDbFromBiomart(
                    ,biomart ="fungi_mart_22"
                    ,dataset = "spombe_eg_gene"
                    ,host="fungi.ensembl.org"
                    )

        Comment

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