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  • Anyone seen an intensity plot like this?

    This is the PhiX lane--anyone seen bases diverge like this? What would cause this? Thanks


  • #2
    Image comin' up blank for me!

    Comment


    • #3
      That's weird--I can see it.
      You could try clicking this link:
      img144.imageshack.us/img144/734/picture3wz7.png

      Comment


      • #4
        Hrm, can see it now.

        I haven't looked at enough intensity plots to know.

        Comment


        • #5
          looking in isolation -

          looks like you have a very weak chip - or a weakish chip with very high signal loss and you are out of signal by the middle of the read. what is the signal loss rate ?

          Comment


          • #6
            Did you use all defaults for the solexa pipeline? Chastity filter of 0.6?
            Mid way through the read, there comes a point where A and C, G and T become quite dependent on each other, and the pipeline uses all kinds of matrices to call one from the other.

            What is the dna sample, if I may ask!
            --
            bioinfosm

            Comment


            • #7
              Did you use all defaults for the solexa pipeline? Chastity filter of 0.6?
              Mid way through the read, there comes a point where A and C, G and T become quite dependent on each other, and the pipeline uses all kinds of matrices to call one from the other.

              What is the dna sample, if I may ask!

              Huh?

              The only corrections the Solexa pipeline performs are crosstalk and phasing corrections. Crosstalk is determined from the first cycle only, and the same matrix is applied to all cycles. The Phasing correction is cycle dependent but is unlikely to cause anything like this.

              Would need to see more plots (all intensities/called intensities) in order to figure out what's happening in this case.

              Comment


              • #8
                Thanks, guys--the plot was for the PhiX control. Tech support thinks we had a focussing issue. Anyway, it didn't happen on the next run.

                Comment

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