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  • 1 lane per treatment vs. multiplexing for rnaseq

    Hi all,

    I ran a pilot for an experiment which had 3 treatments using 1 lane per treatment . We have funds to pay for 3 more full lanes of sequencing. My question is

    Should I run each treatment as I did for the pilot ( using 1 lane per treatment)

    or

    Should I multiplex and run all 3 treatments on each of the sequencing lanes?

    Would I roughly get the same coverage as running a single treatment per lane?

    Any insight would be greatly appreciated.

    nsl

  • #2
    you should multiplex to prevent any technical bias from the lane.

    Have a look at this very nice paper on that.

    Auer, P. L., & Doerge, R. W. (2010). Statistical design and analysis of RNA sequencing data. Genetics, 185(2), 405–416. doi:10.1534/genetics.110.114983

    Comment


    • #3
      thank you

      Comment

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