Hi Guys
I would like to know what the --time-series option in cuffidff does and how it is different from standard differential analysis cufflinks does. I have a time series RNA-Seq experiment where we would like to study the difference in an isoform expression at different timepoints and I understand doing a pairwise differential expression for each condition might not be a good idea for this.
Also how does one go about summarizing --time-series result in cummeRbund to infer differentially expressed features across a time-series experiment. Any help appreciated.
Best,
-Abhi
I would like to know what the --time-series option in cuffidff does and how it is different from standard differential analysis cufflinks does. I have a time series RNA-Seq experiment where we would like to study the difference in an isoform expression at different timepoints and I understand doing a pairwise differential expression for each condition might not be a good idea for this.
Also how does one go about summarizing --time-series result in cummeRbund to infer differentially expressed features across a time-series experiment. Any help appreciated.
Best,
-Abhi
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