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  • Haumich
    Junior Member
    • Jul 2015
    • 5

    #1

    explaining gaps in CBS

    I was performing CNV calling with cnvKIT and pureCN on targeted RNA-Seq data. Both use the CBS-algorithm for segmentation. The segments are usually uniform over all chromosomes, except for one specific gap. I am trying to figure out, what caused this. The coverage of the targets surrounding the gap is not lower compared to other regions on this chromosome.

    Any Idea why there is a gap in this place?
    Click image for larger version

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