cuffdiff : time series and cummeRbund analysis

[apratap]

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

[menorcac]

Time series analysis

Hi,
I came across your post while looking up options to analyse RNA seq data from different time points, and was wondering if you could give me any suggestions about it. I know your post is really old, but any suggestions would be appreciated Thanks!