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• peterbengkui

[peterbengkui]

HPeak usage:
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:

1. Default species is HUMAN. Also supports MOUSE. Can add any other genome if in need.
2. Default format is BED. Also support ELAND. Will add SAM and BAM.
3. –r specifies read length (this is import through my experience).
4. –pe indicates pair-ended data.
5. If data is pair-ended, -isize refers to insert size (total length of a pair).
6. By default, control data is pair-ended if treatment data is pair-ended. Use “-sec”
   if the control data is single-ended for pair-end ChIP data.