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==FindPeak 4.0== * Peak calling using FindPeak 4.0. The reason why MACS1.4 wouldn't work because MACS14 "shifts" read toward the center when reads are pileup on the forward strand and reverse strand. This shifting model wouldn't work for finding enrichment of certain regions in the genome (unlike motif finding, the size of the region is unknown and may be very large). for f in normalized.*BED do awk '{print $1"\t"$2"\t"$3"\t"$4"\t0\t"$6}' $f > tmp java -Xmx2G -jar /usr/local/fp4/FindPeaks.jar -input tmp -aligner bed -output . -wig_step_size 1 - dist_type 0 350 -subpeaks 0.5 -landerwaterman 0.001 -name $f -one_per done; * Number of peaks called for each dataset: 41109 normalized.R.cac.BED_fixed_350_subpeaks.peaks 820 normalized.R.dnmt3a.BED_fixed_350_subpeaks.peaks 12382 normalized.R.fc.BED_fixed_350_subpeaks.peaks 14825 normalized.R.hmc.BED_fixed_350_subpeaks.peaks 28826 normalized.R.mc.BED_fixed_350_subpeaks.peaks 1301 normalized.R.tdg.BED_fixed_350_subpeaks.peaks 2177 normalized.R.tet2.BED_fixed_350_subpeaks.peaks 61289 normalized.S.cac.BED_fixed_350_subpeaks.peaks 1431 normalized.S.dnmt3a.BED_fixed_350_subpeaks.peaks 9107 normalized.S.fc.BED_fixed_350_subpeaks.peaks 51385 normalized.S.hmc.BED_fixed_350_subpeaks.peaks 52640 normalized.S.mc.BED_fixed_350_subpeaks.peaks 1222 normalized.S.tdg.BED_fixed_350_subpeaks.peaks 1090 normalized.S.tet2.BED_fixed_350_subpeaks.peaks * Things to note: For all properly paired reads there are fewer peaks for ChIP data than for dIP data. This is expected since the ChIP are peaks for DNA binding proteins (they are specific). Whereas for the dIP data, it is possible to have more signals since there are many location for cytosines to be oxydized. * I also used the same normalization and peak calling method (except with dist_type 0 110) for the improperly paired reads. 16759 normalized.R.cac.BED_fixed_110_subpeaks.peaks 95 normalized.R.dnmt3a.BED_fixed_110_subpeaks.peaks 4250 normalized.R.fc.BED_fixed_110_subpeaks.peaks 1720 normalized.R.hmc.BED_fixed_110_subpeaks.peaks 2047 normalized.R.mc.BED_fixed_110_subpeaks.peaks 94 normalized.R.tdg.BED_fixed_110_subpeaks.peaks 130 normalized.R.tet2.BED_fixed_110_subpeaks.peaks 16148 normalized.S.cac.BED_fixed_110_subpeaks.peaks 112 normalized.S.dnmt3a.BED_fixed_110_subpeaks.peaks 1688 normalized.S.fc.BED_fixed_110_subpeaks.peaks 1097 normalized.S.hmc.BED_fixed_110_subpeaks.peaks 1212 normalized.S.mc.BED_fixed_110_subpeaks.peaks 109 normalized.S.tdg.BED_fixed_110_subpeaks.peaks 104 normalized.S.tet2.BED_fixed_110_subpeaks.peaks * Things to note: much fewer peaks found for ChIP data, which is expected, since DNMT3a, TDG, and Tet2 are not known to bind in repeats. Up to 10x greater signals are observed for caC marks in both resting and stimulated neurons.
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