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Old 11-27-2011, 03:41 PM   #1
sheenams
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Location: Seattle, Washington

Join Date: Oct 2011
Posts: 15
Default 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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cuffdiff, galaxy, rna seq

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