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.
PS: cross posted on seqanswers : http://seqanswers.com/forums/showthread.php?p=81044#post81044