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Cuffdiff performs differential transcript abundance analysis for two or more RNA-Seq samples. This updated version of the CuffDiff app does not include steps to run CummerBund.
- To use Cuffdiff2, import your BAM files and your GTF file
- Resources: http://cufflinks.cbcb.umd.edu/, http://cufflinks.cbcb.umd.edu/tutorial.html and http://cufflinks.cbcb.umd.edu/howitworks.html#hdif
Use the following files from the directory above as test input:
Parameters Used in App
When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.
- Default parameters only, and WT vs hy5 sample names
Expect a series of files describing the expression for genes and transcripts as output in a cuffdiff_out directory and a series of sorted files of significantly features that have significantly different expression in the sorted_data directory.