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  • keliu.iluke
    Junior Member
    • Jul 2014
    • 4

    #1

    DNase footprint

    Hello, could any one explain when analyzing the DNase footprint, why only the 5-prime end of the DNase-seq read is considered? Given a genomic position, if there are reads whose 3-prime could be mapped to it, why those reads were not considered as cut events? I guess the DNase-seq should NOT be strand-specific.....
  • EricHaugen
    Member
    • Sep 2009
    • 13

    #2
    In DNase-seq the 5' end of a read represents the position and strand where the DNaseI enzyme made a single-stranded cut. This figure may help:

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