Changes between Version 23 and Version 24 of SOPs/InProgress


Ignore:
Timestamp:
05/14/14 10:36:20 (11 years ago)
Author:
gbell
Comment:

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  • SOPs/InProgress

    v23 v24  
    3838# outfile.prefix => the one-word name of your analysis
    3939# min.overlap.ratio => fractional bp overlap (0 to 1) between peaks in replicates to be considered as overlapping peaks. (0 is recommended) 
    40 # is.broadpeak => Is the peak file format broadPeak (or else is narrowPeak)? (F for false)
     40# is.broadpeak => Is the peak file format broadPeak (or else is narrowPeak)? (F for false)  The IDR method is not recommended for broad peaks.
    4141# ranking.measure => p.value is recommended
    42 #
    4342
    4443batch-consistency-analysis.r IP.1_vs_control.1.regionPeak.gz IP.2_vs_control.2.regionPeak.gz -1 rep1_vs_rep2_IDR 0 F p.value chromInfo.txt