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Apply Idr On List Of Read Counts
Entering edit mode
16 months ago
United Kingdom

Does anybody know how to apply the IDR code on lists of read counts per peak, instead of the usual narrowPeak format:

peak-1    20
peak-2    25
peak-3    23

So that using IDR and my peak counts, I get a threshold of the minimum peak intensity for my samples?

I suppose the best version to use is the one explained below, as seen on this url:

(1) batch-consistency-analysis.r

Rscript batch-consistency-analysis.r [peakfile1] [peakfile2] [peak.half.width] [outfile.prefix] [min.overlap.ratio] [is.broadpeak] [ranking.measure]

Typical usage for SPP peak caller peaks
Rscript batch-consistency-analysis.r [peakfile1] [peakfile2] -1 [outfile.prefix] 0 F q.value

Typical usage for MACSv2 peak caller peaks
Rscript batch-consistency-analysis.r [peakfile1] [peakfile2] -1 [outfile.prefix] 0 F p.value

[peakfile1] and [peakfile2] are the peak calls for the pair of replicates in narrowPeak format. They must be uncompressed files.
e.g. /peaks/reps/chipSampleRep1_VS_controlSampleRep0.narrowPeak AND /peaks/reps/chipSampleRep2_VS_controlSampleRep0.narrowPeak

Any ideas?

Entering edit mode
Entering edit mode
16 months ago
Ying W ♦ 3.9k
South San Francisco, CA

I think you need a bit more information to call IDR. It is possible to convert your file of peaks to to a narrowPeak-like format by adding artificial non-overlapping chromosome locations however I think IDR works best with SPP output. You could try posting to their google groups page, the author (Anshul) is pretty active on there.


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