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  • differential expression for de novo

    is there any reccomended tool for finding differential expression for de novo discovery?

    thanks

  • #2
    Originally posted by papori View Post
    is there any reccomended tool for finding differential expression for de novo discovery?

    thanks

    I guess that this is nearly impossible. To compare transcripts, they must either have the same positions in case and control (for all exons of a transcript) or you need a kind of similarity measure over the genomic positions (in respect to intron exon structure). This problem is feasible. The bigger problem is the sequencing depth. You have to 'sequence very very deep' to assemble rare transcripts properly. But if there is really a tool for that, I'm interested, too!

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    • #3
      what i am looking for is just a tool that can find the differential between 2 samples..
      i have already the expression value for each transcript in both samples..
      i just want a tool that know which transcripts have the same sequence(~).. and can compare there expression value.
      i dont understand why do i need genome for that?
      i just want to find the difference between those 2 samples..
      thanks

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