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  • pmiguel
    replied
    I've never understood why people think that pair-merging prior to de novo assembly is a good idea. Seems like were that the case, assembly engines would just do pair-merging themselves prior to other assembly steps.

    --
    Phillip

    Leave a comment:


  • GenoMax
    replied
    For reference cross-posted to: https://www.biostars.org/p/295213/

    Leave a comment:


  • roussine
    started a topic Merging PE reads before de novo RNA-Seq assembly

    Merging PE reads before de novo RNA-Seq assembly

    Hello!
    can someone please give an opinion: does that make sense to merge PE reads before a de novo RNA-seq assembly (say with Trinity)?
    Merging tools are quite fast (like USEARCH www.drive5.com/usearch/manual/merge_pair.html), and the amount of raw data is reduced drastically. Can merged data be suitable for further assembly in a “single-ends” mode, or am I missing some theory behind it?.. Seems like it may save a lot of computations.

    Thanks in advance.
    Leo

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