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  • cuffdiff : time series and cummeRbund analysis

    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

  • #2
    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!

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