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Question: Cuffcompare Outputs Missing
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gravatar for i b
6.4 years ago by
i b • 330
i b • 330 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???) Thanks, ngs-ib
rna-seq cufflinks • 1.3k views
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modified 6.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.4 years ago by i b • 330
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gravatar for Jennifer Hillman Jackson
6.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
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- implementation-td4139721.html Best, Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org
ADD COMMENT • link written 6.4 years ago by Jennifer Hillman Jackson ♦ 25k
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