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  • RNAseq peak calling

    I have some sncRNA seq datasets and would like to identify differentially expressed regions.

    The problem is that the interesting regions may not previously have been annotated, so mapping to existing sncRNA genes and then analyzing those is not an option.

    I was thinking of splitting the genome into ~50nt bins, mapping to those and then doing DE analysis on the bins.

    Is there a better way? Would it be possible to use the tools for ChIP peak calling?

    I am a little new at this so even a nudge in the right direction would be appreciated.

  • #2
    It seems that Cufflink:



    does exactly what I wanted to do.

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