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  • about the duplication sequence in the whole transcriptome

    Hi all,

    I use the data to analysis the denovo transcriptome, it is consider that the high duplication rate will lead bad results.

    As we konw the multiple similar sequences(duplicates) due to PCR amplification, and some from the really high self-expression. How to separate these from the false PCR-based duplicaiton?

    I want to know how to define the duplicaiton sequence for whole transcriptome sequencing?
    I am wonder whether it is meaningful to count the duplication rate in the denovo whole transcriptome as a control data standards. If so, could you please tell me how much the dup rate is considered normal ?

    if someone know,please let me know


    Best Regard!

  • #2
    Maybe you can try Picard and samtools.

    Comment


    • #3
      Originally posted by zhangww View Post
      Hi all,

      I use the data to analysis the denovo transcriptome, it is consider that the high duplication rate will lead bad results.

      As we konw the multiple similar sequences(duplicates) due to PCR amplification, and some from the really high self-expression. How to separate these from the false PCR-based duplicaiton?

      I want to know how to define the duplicaiton sequence for whole transcriptome sequencing?
      I am wonder whether it is meaningful to count the duplication rate in the denovo whole transcriptome as a control data standards. If so, could you please tell me how much the dup rate is considered normal ?

      if someone know,please let me know


      Best Regard!
      FastQC also runs a check for duplication and report the total duplication value with a warning if too high!

      Comment

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