I have just loaded the latest CummeRbund program v2.01 and have a few questions. My RNAseq data is from 3 time points where each timepoint has a control C1, C2, C3 and an experimental condition E1 , E2 and E3. I have created cuffdiff output for all pairwise comparisons C1_E1, C2_E2, C3_E3. Should I save all cuffdiff output into a single directory for creating plots for all conditions? Also how do you save plots that are generated with CummeRbund?
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Originally posted by godzilla07 View PostI have just loaded the latest CummeRbund program v2.01 and have a few questions. My RNAseq data is from 3 time points where each timepoint has a control C1, C2, C3 and an experimental condition E1 , E2 and E3. I have created cuffdiff output for all pairwise comparisons C1_E1, C2_E2, C3_E3. Should I save all cuffdiff output into a single directory for creating plots for all conditions? Also how do you save plots that are generated with CummeRbund?
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