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Old 11-18-2011, 01:59 AM   #1
SEQond
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Default Cuffdiff Gene Expression. ideal minimum number of alignments

how to identify the ideal -c "minimum number of alignments in a locus for needed to conduct significance testing" (--min-alignment-count) to be used in cuffdiff?
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Old 12-16-2011, 01:10 PM   #2
sepulveda
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I want to find out too, the default is 1000. How do we set the best value for different RNA-Seq data? Anyone can answer this?
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Old 12-16-2011, 03:28 PM   #3
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The default, when using Galaxy, is set to 1000. However, the documentation says this value is set to 10 by default. I'm curious as to this discrepancy and the best value for RNA Seq experiments.


-c/--min-alignment-count <int> The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not signficant, and the locus' observed changes don't contribute to correction for multiple testing. The default is 10 fragment alignments.
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Old 12-16-2011, 07:08 PM   #4
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Hi, yes, I noticed that too... was it a mistake on the documentation or on Galaxy? but I had set 100 on my data.
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Old 05-08-2012, 07:12 AM   #5
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Galaxy just changed it to 10, seems a mistake.
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