pomoda

/ Pomoda: Peak Oriented Motif Discovery Algorithm http://compbio.ddns.nus.edu.sg/~chipseq/Pomoda Function: generates position weight matrixes (PWM) for motifs concentrate around the ChIP-Seq peaks Syntax: POMODA -i inputFasta -o outputDIR [-w weightFile, -ot overlapThreshold -pdt PWM\_Divergence\_Threshold **-ratio minSupportRatio, -FDR p-valueCutoff, -maxlen maxMotifLength, -seedlen SeedLength,-rs resolution\_bp, -mbr min\_binding\_range** -n numberOfMotifs] Comments: inputFasta: input data, using fasta format, recommended length per sequence is 10k outputDIR: the directory for output of one task, different task should have different outputDIR, otherwise, the output position file will be replaced. weightFile: the file store the peak intensity, each line corresponding to one sequence in inputFasta, e.g., ":3251" in the 1st line, says the first sequence intensity is 3251, [optional](optional.md)