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  • prediction-free differential exon-usage analysis

    Hi all,

    I have a RNAseq data set from the drosophila genome without replica. I would like to run a differential exon-usage analysis on this data set.

    The genes we are interested in are poorly annotated, so I am looking for a tool which can work without relying on predicted transcripts.

    I have found out the cufflink-cuffdiff package can work without replica and run the analysis without relying only on the gtf file, but I would like to know if there are other tools out there who can do the same analysis, but on a friendlier way.

    thanks
    Assa

    PS
    I have posted a similar question on biostar, but I hope to get here different responses.

  • #2
    I don't know of a better analysis package, but BBMap is good for unbiased RNA-seq mapping that does not rely on existing gene annotations.

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    • #3
      thanks for the reply

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