Good catch, Kevin. Galaxy tool wrappers generally use default tool parameter 
values, so either the default value of this parameter changed from previous 
versions of Cuffdiff or this was a bug. Either way, it's been fixed in our code 
repository and will be available on our public server shortly.


On Apr 27, 2012, at 6:06 PM, Kevin Silverstein wrote:

> Hi Galaxy Developers,
> This is regarding the wrapper for cuffdiff and the –c parameter for “Min 
> alignment count”.  We noted that Galaxy’s default value is set to 1000.  In 
> our experience, setting this parameter that high yields drastically different 
> results from the ones obtained with the author’s original default value of c 
> = 10.
> The –c parameter is defined as:
> -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.
> We have found that the value entered will require that at least this number 
> of fragment alignments be found for *each* sample (or at least each 
> condition) in order for the locus to be tested for differential expression. 
> Although one could save themselves a lot of locus comparisons (and hence take 
> a much smaller hit for multiple hypothesis testing) if he/she were to raise 
> this threshold, this will screen out the most desirable differentially 
> expressed genes – specifically those that are not expressed at all in one 
> condition but highly expressed in the other condition.
> The attached image has a real example of a gene that was counted as 
> differentially expressed (as it should have been) with ‘10’ but was not even 
> tested at ‘100’ nor ‘1000’.
> -Kevin Silverstein

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