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  • egunth
    started a topic Cufflinks not IDing transcripts correctly

    Cufflinks not IDing transcripts correctly

    Hi all,

    I'm using Cufflinks to calculate transcript abundances on my human RNA seq data but it seems to be having a problem matching transcripts in my data to their correct gene ID's from a reference GTF. I generated a RefSeq hg18.gtf annotation file from the UCSC table browser and loaded that for into cufflinks for all of my samples. About 60% of the loci it processes are labelled with their RefSeq ID, but many of them simply have a generic "CUFF.1" ID attached to them, even though the associated genomic loci are present in my annotation.

    For example, This is what I see in my genes.fpkm_tracking file for one locus

    CUFF.2 - - CUFF.2 - - chr1:4224-19255 - - OK 47.7646 38.9667 56.5625

    But in my annotation that locus is clearly listed as WASH7P

    chr1 hg18_refFlat exon 4225 4692 0.000000 - . gene_id "WASH7P"; transcript_id "WASH7P";
    chr1 hg18_refFlat exon 4833 4901 0.000000 - . gene_id "WASH7P"; transcript_id "WASH7P";
    chr1 hg18_refFlat exon 5659 5810 0.000000 - . gene_id "WASH7P"; transcript_id "WASH7P";
    chr1 hg18_refFlat exon 6470 6628 0.000000 - . gene_id "WASH7P"; transcript_id "WASH7P";
    chr1 hg18_refFlat exon 6721 6918 0.000000 - . gene_id "WASH7P"; transcript_id "WASH7P";
    chr1 hg18_refFlat exon 7096 7231 0.000000 - . gene_id "WASH7P"; transcript_id "WASH7P";
    chr1 hg18_refFlat exon 7469 7605 0.000000 - . gene_id "WASH7P"; transcript_id "WASH7P";
    chr1 hg18_refFlat exon 7778 7924 0.000000 - . gene_id "WASH7P"; transcript_id "WASH7P";
    chr1 hg18_refFlat exon 8131 8229 0.000000 - . gene_id "WASH7P"; transcript_id "WASH7P";
    chr1 hg18_refFlat exon 14601 14754 0.000000 - . gene_id "WASH7P"; transcript_id "WASH7P";
    chr1 hg18_refFlat exon 19184 19233 0.000000 - . gene_id "WASH7P"; transcript_id "WASH7P";

    Am I using the wrong format annotation file for this?

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