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  • aggregate read cycle info from bam files

    Hi Everyone:

    I am trying to obtain this plot from some SNPs of my samples. You can see the plot in 8.52 of this video (R.Irizarry group) :

    Basically, I need to know the cycle of each aligned read in a given position. I am thinking in indirect solutions ( I am using Illumina reads, 90bp ) but I was wondering if anyone have done these plots, or know some tool to directly extract this information ( in principle from a Bam File ).

    Thank you very much
    Oriol

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