Monday, 24 August 2015

FeatureCounts: Strandedness

From the source code of featureCounts

   """
    0: unstranded 1: stranded 2: reverse stranded
    """
    strand_flag = {"unstranded": "0",
                   "firststrand": "2",
                   "secondstrand": "1"}
    stranded =  get_in(config, ("algorithm", "strandedness"),
                       "unstranded").lower()

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