Hello, The output you describe is correct. If you are going forward with Cuffdiff, the resulting "combined transcripts" dataset will be the input reference annotation. The Cuffcompare wrapper accepts and processes multiple input Cufflinks GTF inputs and creates the Transcripts Accuracy, Transcripts Combined, and Transcripts Tracking files as primary outputs (considering all inputs) and the Tmap and Refmap files for the first two GTF inputs as secondary outputs. A prior thread on the galaxy-dev@bx.psu.edu mailing list discusses the technical reasons behind this implementation in brief: http://dev.list.galaxyproject.org/Question-about-cuffcompare-tool-implementa... Best, Jen Galaxy team On 7/17/12 1:18 AM, i b wrote:

Hi, I ran cuffcompare using 3 samples as inputs (dataset 1-2-3 cufflinks gtf) and a reference annotation (dataset 4). These are the outputs:

5: Cuffcompare on data 1, data 4, and others: transcript accuracy 6: Cuffcompare on data 1, data 4, and others: 1 data tmap file 7: Cuffcompare on data 1, data 4, and others: data 1 refmap file 8: Cuffcompare on data 1, data 4, and others: data 2 tmap file 9: Cuffcompare on data 1, data 4, and others: data 2 refmap file 10: Cuffcompare on data 1, data 4, and others: transcript tracking 11: Cuffcompare on data 1, data 4, and others: combined transcripts

my question: why I don't have tmap and refmap on dataset 3?Why only 1 and 2 (arbitrary???)

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