Hello Daiene,

You might try starting with adding in "Perform quartile normalization: Yes", if not already using. Although, if 95% of your data is exceeding the HIDATA threshold, this may not have much effect. Another option is to reduce the number of replicates.

And yes, this is a configurable option, but not on the Cuffdiff tool as implemented on the main public Galaxy instance. In order to modify away from the default option, a local instance would be needed along with this parameter to the tool wrapper. http://getgalaxy.org

For a list of available Cuffdiff options, scroll to the bottom of the tool form to see the section:

Cuffdiff parameter list
This is a list of implemented Cuffdiff options

Next, to see where this is an option in the Cuffdiff tool itself, follow the links on the Galaxy CuffDiff tool form (or google search "cuffdiff HIDATA") to bring up the home page for the tool at http://cufflinks.cbcb.umd.edu/manual.html. Then perform a "find" on the keyword "HIDATA" to locate:

--max-bundle-frags <int> Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are marked with status HIDATA. Default: 1000000

Hopefully this helps! Next time, sending a question to one mailing list is sufficient - no need for duplicating.

Best,
Jen
Galaxy team

On 7/6/12 6:31 AM, Daiene Santos wrote:

After running Cuffdiff, I got more than 95% of genes with HIDATA status.

What should I do?

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