I'm new to bioinformatics and I have what seems like a weird task. I have 7 samples of a fungus with 2 replicates each. I want to compare 1 of these samples vs all 6 of the rest. However I'm not sure how to set this up.
Would I basically do cuffdiff -L group1, group2 sample1r1,sample1r2 sample2r1,sample2r2,sample3r1,sample3r2... and put them all in the same group and treat them all like replicates? This doesn't seem right, but I haven't found a better way to group them.
Would I basically do cuffdiff -L group1, group2 sample1r1,sample1r2 sample2r1,sample2r2,sample3r1,sample3r2... and put them all in the same group and treat them all like replicates? This doesn't seem right, but I haven't found a better way to group them.
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