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Old 02-04-2013, 05:30 PM   #1
mshamblott
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Location: florida

Join Date: Feb 2013
Posts: 8
Default Pool cuffdiff output -exp.diff files?

The four DE output files isoform_, gene_, tss_groupd_ and cds_exp all address different levels of pooling matches between RNAseq reads and genome.

I have genes of known DE (QPCR) scattered in all 4 .diff files. To make a list of ALL putative DE genes identified by cuffdiff should I blend the results from all 4 .diff files? Here is my post-cuffdiff workflow:

1. Copy 4 .diff files into excel tabs. The non_exp .diff files have nothing significant.
2. filter for significance
3. copy all significant rows into a new tab.
4. copy all significant rows into one combined tab.
5. sort out duplicates from combined list
6. filter on fold change to rank.

This fails to calculate a mean of numeric values and is a pretty round-a-bout way to get a simple fold change list.
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