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A HMM-based algorithm for defining enriched regions from ChIP-seq data
... 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).
Support for the Oasis XRI (Extensible Resource Identifiers) effort. This includes resolvers and client libraries for XRIs in multiple languages and multiple platforms. See http://www.oasis-open.org/committees/xri