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  • #1

    Tophat result: how to get the number for novel junctions

    hi,

    tophat can output a file junctions.bed including the splicing sites for junction reads.
    Can I get novel splicing sites that tophat identified from known ones given by reference gene annotations?
    Any suggestions would be appreciated.
    Tags: junctions, splicing annotation, tophat 2.0.8b
  • #2
    can cuffdiff handle the samples with different treatments and a time series?

    any suggestions?
    Last edited by Triple_W; 07-02-2013, 11:51 PM.

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