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  • what an interesting base distribution plot!

    Have you seen such base distribution plot in BS-seq?
    Attached Files

  • #2
    If by BS-seq you mean Bisulfite Sequencing I have to say NO. Conversion has failed or all Cs were methylated!

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    • #3
      I concur with nucacidhunter and add "Yikes, that's bad!"

      Comment


      • #4
        If the experiment is 2x125bp paired-end sequencing and both were concatenated into this one plot and the sequencing is non-directional and you used some kind of target enrichment technique or random primed pull-down then there might be a chance that there is something to be had from the data. But only you would know your library that well...
        If this is not the case, I would like to agree with the above posters.

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        • #5
          This plot indicates a very high level of adapter dimer fragments in your library. Filter these out with your favorite trimming/filtering tool and then repeat the base composition plot to see what your valid library fragments look like.

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