readme

JAMM is a universal peak finder for NGS datasets that can integrate information from biological replicates. 

JAMM was developed in the Ohler lab at the Berlin Institute for Medical Systems Biology.


Visit this page for documentation: https://github.com/mahmoudibrahim/JAMM
Also check JAMM's publication in Bioinformatics: http://bioinformatics.oxfordjournals.org/content/31/1/48


To install JAMM:
- Make sure you are on a Linux system
- Make sure you have R and Perl installed
- Install the following R packages: signal and mclust 


To get information about options available to JAMM users, run the JAMM bash script without any parameters or visit the documentation page at https://github.com/mahmoudibrahim/JAMM/wiki/Usage


If you encounter errors or have questions, please email mmibrahim@pm.me


Important Note: JAMM produces a large number of peaks on purpose to allow you to choose your threshold the way you like. The peaks are scored and ranked by column 7  in the output narrowPeak file. If you want a confident list directly from JAMM, you could use the option "-e auto", although a better way is probably to see the peaks that are reproducible in your replicates.