A HMM-based algorithm for defining enriched regions from ChIP-seq data
HPeak is a hiddenMarkov model-based approach that can accurately pinpoint regions to where significantly more sequence reads map. Testing on real data shows that these regions are indeed highly enriched by the right protein binding sites.
Command (single-end):
perl /compbio/software/HPeak3/HPeak.pl -sp HUMAN/MOUSE -format BED -t TREATMENT.inp -c CONTROL.inp -n OUTPUTPREFIX -fmin 100 -fmax 300 -r 36 -ann -wig -seq -interfiles
Command (pair-end):
perl /compbio/software/HPeak3/HPeak.pl -sp HUMAN/MOUSE -format BED -pe TREATMENT.inp -c CONTROL.inp -n OUTPUTPREFIX -isize 200 -r 100 -pec (if control is PE) -ann -wig -seq –interfiles
note:
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