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  • letusgo
    Member
    • Aug 2011
    • 17
    #1

    How to do alignment quality control?

    I alignment my clean reads to my reference genes using Tophat, then I want to know if it did well. so I want to get the Distribution of reads on reference genes and the sequencing saturation analysis.Finally, I need to draw two figures like below. How can I do it, is there any soft can solve my problem?
    Thank you
    Click image for larger version Name: 1.jpg Views: 1 Size: 37.8 KB ID: 307930

    Click image for larger version Name: 2.jpg Views: 1 Size: 47.8 KB ID: 307931
    Tags: alignment, mapping, quality control
    • jialicd
      Junior Member
      • Oct 2012
      • 1
      #2
      same question. but you can try R to plot .

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