TALENPWMScorer

Dependencies

• g++
• python

Build

git clone https://github.com/andynu/TALENPWMScorer.git
git submodule init
git submodule update
./make.sh

Run

Usage: ./findTALENPairsInGenome.py seqDir mode1 motifDef1 modeParam1 topN1 minSpacer maxSpacer mode2 motifDef2 modeParam2 topN2 outDir
seqDir 
mode1 
  "consensus"
    provided desired bind sequence
  "PWM"
motifDef1 
  if mode1 "consensus"
    provided desired bind sequence
  if mode1 "PWM"
  filename that provides the position weight matrix
modeParam1 
  if mode1 "consensus"
    number of mismatches 
  if mode1 "PWM"
    minimum score
topN1 
  number of sites to output
minSpacer 
  number
maxSpacer 
  number
mode2
  "consensus"
    provided desired bind sequence
  "PWM"
motifDef2
  if mode2 "consensus"
    provided desired bind sequence
  if mode2 "PWM"
  filename that provides the position weight matrix
modeParam2 
  if mode2 "consensus"
    number of mismatches 
  if mode2 "PWM"
    minimum score
topN2g 
  number of sites to output
minSpacer 
  number
maxSpacer 
  number
outDir