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  • compare distribution of coverage in solexa data

    Hi (i'm new in this forum and new in sequencing analysis, please be patient )

    I’m comparing some solexa re-sequence experiment in which different DNA sharing treatment were used.

    I there any statistic I can use to compare coverage evenness between sequencing experiments?

  • #2
    Originally posted by scuellar View Post
    Hi (i'm new in this forum and new in sequencing analysis, please be patient )

    I’m comparing some solexa re-sequence experiment in which different DNA sharing treatment were used.

    I there any statistic I can use to compare coverage evenness between sequencing experiments?
    Assuming you have some ref sequence: Map your data with your aligner of choice and generate (S|B)am output. After that, pileup the alignments with samtools. Use column number 2 and 8 in the pileup to find out what's the reference coordinate and the number of reads covering the position. Then plot that with gnuplot (or R).
    -drd

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    • #3
      Thanks Drio

      Very helpful. Now i solved the problem the solutions sound so evident

      Thanks again

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      • #4
        Or you could use something like IGV or USCS to visualize the coverage information.
        --
        bioinfosm

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