Boioinformatics Tips: Contrast file for cuffdiff

Cuffdiff, by default, compares each pair of conditions in your experiment. If you have many conditions, this can create a lot of additional work for the program. These extra conditions can cause Cuffdiff's output files to be very large, which can slow down CummeRbund and other downstream analysis software. Often, you are not interested in all pairwise contrasts. Rather, you'd like to compare all conditions to a common control, or only look at matched pairs of samples. You can specify the contrasts Cuffdiff should perform using a contrast file.

Contrast files are simple, tab delimited text files. They should have a single header line as the first line in the file, followed by one line for each contrast you'd like to perform. The files should have two columns, as specified below:

Column number	Column name	Example	Description
1	condition_A	Ctrl	A condition label. Must match one of the labels specified through -L or in the sample sheet.
1	condition_B	Ctrl	A condition label. Must match one of the labels specified through -L or in the sample sheet.

To run Cuffdiff with a contrast file, simply provide the -C <contrasts.txt> option at the command line. 
An example table might look like this:

condition_A condition_B
Ctrl Mutant_X
Ctrl Mutant_Y
Ctrl Mutant_Z