Canadian Epigenetics, Environment and Health Research Consortium

ChIP-Seq Post Processing

Peak calling for each assay is done with FindER version 1.0.1e using the following comamd line:
java -jar -Xmx30G FindER.1.0.1e.jar -signalBam $TREAT -inputBam $CONTROL -out $OUT


Two post processed tracks are generated:

peaksEnrichment calls are formatted as a bigBed file.
peaks_bwEnrichment calls are formatted as a bigWig file where enriched regions are assigned a score of 1 and 0 otherwise. This is done for compact visualization over long genomic stretches when compared to "peaks" track type.