Basic Tutorial

Before going ahead with this tutorial, please make sure JAMM is running properly on your machine using the small dataset provided here.

The purpose of this tutorial is to help you get started with running JAMM. The tutorial uses ENCODE (Broad Institute) H3K27ac ChIP-Seq full dataset from HeLa-S3 cells.

It starts with the aligned BED files which we provide here. Those files were generated by aligning reads to hg19 using Bowtie2, followed by PCR duplicates removal using SAMtools.

Step 1: Download the H3K27ac ChIP-Seq BED files corresponding to Replicate 1, Replicate 2 and ChIP Input (Warning: Files are big, up to about 4Gb).

• Replicate 1

• Replicate 2

• ChIP HeLa-S3 Broad Institute Input

Step 2: Download the chromosome size file corresponding to hg19 genome build. This file is needed by JAMM to run.

• hg19 chromosome size file

Step 3: Create the directory structure you need to run JAMM. We recommend you set up a main directory called "H3K27ac" and 2 additional sub-directories called "sample" and "control":

mkdir H3K27ac

mkdir H3K27ac/sample

mkdir H3K27ac/ctrl

Step 4: Copy the Replicate 1 and Replicate 2 BED files to the H3K27ac/sample directory. Copy the Input file to the H2K27ac/ctrl directory.

Step 5: Copy the chromosome size file to the H3K27ac directory.

Step 6: You are now ready to run JAMM:

bash /path/to/JAMM/folder/JAMM.sh -s /path/to/your/"H3K27ac/sample"/folder -g /path/to/your/chromosome/size/file -o /path/to/folder/with/your/main/"H3K27ac"/folder -c /path/to/folder/with/your/"H3K27ac/ctrl"/folder

Step 7: Check the output. You will have two new folders in your main H3K27ac directory. One is called peaks containing your peak files and one is called xcorr containing results for cross-correlation analysis.

We already analyzed this dataset using JAMMv1.0.4 and you can get our results here (Provided just as an example, not to be used directly in publications!).

More information about JAMM output is provided on the Usage Wiki page