I am a bit confused on how to run tophat/cufflinks properly. I have (paired) RNAseq data from pig. I have 8 samples (4 disease, 4 control). For each sample I also have data from 2 lanes (so was each sample run twice?)
I want to ultimately do differential expression analysis using cuffdiff.
When I run tophat do I input all of the reads I have into one tophat command?
e.g. tophat Sample_1/left_read, Sample_2/left_read, ... Sample_1/right_read, Sample_2/right_read
or do I run 8 separate tophat runs
tophat Sample_1/left_read Sample_1/right_read
tophat Sample_2/left_read Sample_2/right_read