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  • cummeRbund gene tracking

    Hello,

    I am having an issue with gene tracking in cummeRbund. The following happens:

    > genetrack <- makeGeneRegionTrack(myGene)
    Error in `[.data.frame`(features(object), , featCols) :
    undefined columns selected

    I am using an Ensembl gtf and have set

    > options(ucscChromosomeNames=FALSE),

    but no luck. I have also tried using the cummeRbund cufflinks data from the sample directory

    a<-readCufflinks(system.file("extdata", package="cummeRbund"))

    but still no luck. I have no issue analyzing 'myGene' or any other cummeRbund feature, so I assume I've accessed the data correctly. Any ideas on what the problem might be?

    Thanks.

  • #2
    Hi:
    any luck with
    genetrack<-makeGeneRegionTrack(myGene)


    > myGeneId<-"XLOC_000672"
    > myGene<-getGene(cuff,myGeneId)

    > head(features(myGene))
    [1] feature_id gene_id isoform_id seqnames source type start end score strand frame
    <0 rows> (or 0-length row.names)



    In merged.gtf file obtained after cuffmerge, I find that the same gene/transcript exists.

    chr1 Cufflinks exon 18164443 18164555 . - . gene_id "XLOC_000672"; transcript_id "TCONS_00000699"; exon_number "2"; gene_name "NM_001114847"; oId "NM_001114847"; nearest_ref "NM_001114847"; class_code "="; tss_id "TSS675"; p_id "P442";


    In that case why I see features(myGene) is empty.

    It is frustrating in deed.
    -Adrian

    Comment


    • #3
      It works this way!!!!

      cuff<-readCufflinks(gtfFile='myTranscriptome.gtf',genome='mm9',rebuild=T)



      Application of sequencing to RNA analysis (RNA-Seq, whole transcriptome, SAGE, expression analysis, novel organism mining, splice variants)

      Comment


      • #4
        Hello Adrian, I am struggling with this too, does that mean you have to have the gtf file and the genome? Do you use genome.fa ? genome after you run bowtie-build?

        Thanks

        Comment

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