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==SISSRs== * Peak calling using SISSRs (a simple perl script)..FDR calculated from a Poisson distribution. for f in normalized*.BED do sissrs.pl -i $f -s 2654911517 -m 0.7 -F 350 -u -D 0.001 -o $f.peaks done; -i (input BED file) -s (genome size in bp) -m (fraction of genome covered, estimated 0.7) -F (average fragment length, inferred from sampe.log (BWA) the median is 300, and average could be 350. -u (report peaks which is not supported by at least two reads in both directions as well) -D (FDR, 0.001) -o (output peak file) * Peaks for properly paired reads: 8131 normalized.R.cac.BED.peaks 474 normalized.R.dnmt3a.BED.peaks 7418 normalized.R.fc.BED.peaks 8838 normalized.R.hmc.BED.peaks 21352 normalized.R.mc.BED.peaks 565 normalized.R.tdg.BED.peaks 806 normalized.R.tet2.BED.peaks 7300 normalized.S.cac.BED.peaks 653 normalized.S.dnmt3a.BED.peaks 5653 normalized.S.fc.BED.peaks 33480 normalized.S.hmc.BED.peaks 32660 normalized.S.mc.BED.peaks 548 normalized.S.tdg.BED.peaks 704 normalized.S.tet2.BED.peaks * Peaks for improperly paired reads (to be done)
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