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  • Trinity-Duplicate removal

    Dear All,

    I am using trinity for transcriptomics assembly. I have few queries:-

    1) have two condition(Control and Treated) and each condition has 4 replicates. so if I merge these .fq files together, how the generated assembly from this merged .fq file would be better than the assembly generated from single(using only one replicate) sample?

    2) Do I need to remove duplicates from individual fastq file before merging or after merging them together?

    3) I saw there is a script "fasta_remove_duplicates" in the trinity folder. So is there any chance that "In-silico-normalization" in trinity take care of these duplicate reads?

    I would appreciate any explanations.

  • #2
    I don't have a direct answer to this, but I think the following links might help you understand what the "In-silico-normalization" is doing :

    [What does Trinity's In Silico normalization do?]
    This post can be referenced and cited at the following DOI: http://dx.doi.org/10.6084/m9.figshare.98198. For a few months, the Trinity list was...

    [What is digital normalization, anyway?]
    I'm out at a Cloud Computing for the Human Microbiome Workshop and I've been trying to convince people of the importance of digital normalization....

    Comment


    • #3
      Thanks yueluo,

      Comment

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