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  • P-Richmond
    Member
    • Oct 2010
    • 13

    visualizing strand-specific read coverage per position

    Hello,
    I'm looking to display strand-specific RNA-seq data coverage data. I currently generate per-position strand specific coverage using genomeCoverageBed (genomeCoverageBed -ibam <in.bam>-d -s +[-]), but I wanted to see if there was a file-format where I could display both coverages in the same file. I imagine something like this:

    chr \t position \t positive_score \t negative_score
    chrI 1 0 0
    chrI 2 0 0
    chrI 3 0 0
    ...
    chrI 30299 29 11
    ...
    chrI 200399 39 2293


    or via the WIG format:
    chr = chrI; step = 1; span=1
    29 -11
    39 -2293

    for every position in the genome.

    Thanks for your help,
    Phil

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