1. Starting Up:

• This has been tested to work in Ubuntu v14.04.4 LTS and Mac OSX v10.9.5
• If you are using Windows, then install Linux using wubi (http://wubi.sourceforge.net/faq.php) - this is easiest.
• If you're using Mac/Linux, then open terminal
• In terminal type git and enter. If it says something along the line command not found then install git from the link below:
  • Mac: https://git-scm.com/download/mac
  • Linux: https://git-scm.com/download/linux
• Then copy paste this below on the terminal to use my default installation path:

# Go to home folder
cd

# Copy the highsenshmm software
git clone https://github.com/srhartono/highsenshmm

# It should start download. Once finished, go to highsenshmm folder
cd highsenshmm

2. Requirements:

1. bedtools v.2.17 (http://bedtools.readthedocs.io/en/latest/content/installation.html)

• To check if you have it or not, in terminal just type bedtools --version.

• If command not found or the version isn't at least v.2.17 then you have to install it.

• To install bedtools copy paste below:

  # go to bedtools folder
  cd bin/bedtools2_25_0/
  
  # make is linux way of installing
  make
  
  # go to main folder
  cd ../../
  

2. stochhmm v. 0.35 (https://github.com/KorfLab/StochHMM)

• To check if you have it or not, in terminal just type stochhmm.

• If command not found or the version isn't at least v.0.35 then you have to install it.

• To install stochhmm copy paste below in the terminal

  # go to bin folder
  cd bin
  
  # git clone StochHMM
  git clone https://github.com/KorfLab/StochHMM
  
  # go to StochHMM folder
  cd StochHMM
  
  # configure is to configure the make according to your computer setup
  ./configure
  make
  
  # go to main folder
  cd ../../
  

• If stochhmm failed to install, I put some binaries inside bin folder for ubuntu or mac which could work

  #Create stochhmm directory in bin
  mkdir bin/StochHMM/
  
  #Copy paste stochhmm according to your operating system (mac/ubuntu)
  cp bin/stochhmm_mac_10.9.5 bin/StochHMM/stochhmm
  cp bin/stochhmm_ubuntu_14.04.4 bin/StochHMM/stochhmm
  

3. Test run:

To quickly test if everything works do:

./Pipeline.pl test.txt > test.log

If it produces an output file (output.txt) then it's success.

Otherwise email me the test.log file

4. How to run:

Say we are running this on ZNF420 region (chr19:37518112-37671921) for 4 DRIPc + strand files (provided in this directory)

• Control: ExampleZNF420_control_pos.wig
• Scramble: ExampleZNF420_scramble_pos.wig
• Top1A: ExampleZNF420_top1A_pos.wig
• Top1B: ExampleZNF420_top1B_pos.wig

Create a text file using whatever text editor you want (recommended: nano, vim, for mac: textedit, textwrangler) and put all 4 file names, one file per row. Example is FILES.txt

ExampleZNF420_control_pos.wig
ExampleZNF420_scramble_pos.wig
ExampleZNF420_top1A_pos.wig
ExampleZNF420_top1B_pos.wig

Then run Pipeline.pl on the text file, for example:

./Pipeline.pl FILES.txt > FILES.log

If there is a green SUCCESS then it's successful, otherwise send me the FILES.log file

This will produce 1 peak file per sample and a combined peak file output.PEAK. For example, the above will produce:

1. ExampleZNF420_control_pos.peak
2. ExampleZNF420_scramble_pos.peak
3. ExampleZNF420_top1A_pos.peak
4. ExampleZNF420_top1B_pos.peak
5. output.PEAK