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  • Cuffdiff output

    I'm using the Tuxedo suite in Galaxy for RNA analysis of Illumina, 30bp single end reads. My mentor would like the output to match what was done in a paired end analysis from a similar experiment, mapped to the Zebrafish Ensembl GTF.

    The previous output looks like this:

    test_id gene_id gene locus sample_1 sample_2
    ENSDARG00000000001 ENSDARG00000000001 slc35a5 9:35060459-35093143 q1 q2
    ENSDARG00000000002 ENSDARG00000000002 ccdc80 9:35060459-35093143 q1 q2
    ENSDARG00000000018 ENSDARG00000000018 nrf1 4:14146776-14169064 q1 q2

    However, the default output of Cuffdiff gives XLOC IDs:

    test_id gene_id gene locus Sample_1 Sample_2
    XLOC_000001 XLOC_000001 ENSDART00000127092 Zv9_NA10:29174-34103 CON REG
    XLOC_000002 XLOC_000002 ENSDART00000130683 Zv9_NA101:39833-39948 CON REG


    How do I map the XLOC IDs to Ensembl IDs for 'gene_id' with gene symbol as the 'gene'? The previous experiment was also mapped to the same Ensembl GTF (or so I've been told), I'm just assuming they did some post-cuffdiff processing of the output files.

    Thanks

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