xinbeibei/jamm

JAMM Peak Finder for Sequencing Datasets

JAMM Peak Finder

JAMM is a peak finder for NGS datasets (ChIP-Seq, ATAC-Seq, DNase-Seq..etc.) that can integrate replicates and assign peak boundaries accurately. JAMM is applicable to both broad and narrow datasets. Read more in JAMM's publication.

JAMM was developed at the Ohler lab at BIMSB-MDC in Berlin.

If you have questions or need help running JAMM please email us at this email, we will be happy to help you.

Download JAMM

The latest JAMM version is JAMMv1.0.7rev4. Click here to download it.

If you are interested in older versions, check the Downloads Archive or the Github release page.

Latest News and Updates

• June 07 2016: New version of JAMM released (v1.0.7rev4). This version has a fix for a minor bug in enriched window finding.

• Mar 28 2016: New version of JAMM released (v1.0.7rev3). This version has some bug fixes with automated threshold calculation that caused it to be very slow and with paired-end handling. Paired-end analysis should now work with this version.

Visit the the Wiki Homepage for older updates and news.

JAMM Documentation

• How to Install JAMM
• How to Use JAMM
• Frequently Asked Questions
• Parameter Recommendations
• Of course it is always good to read the actual paper :)

Please check the Wiki Homepage for more information on JAMM.

If you still have questions or need help running JAMM please email us at this email.

Note: JAMM produces a large list of peaks on purpose so that you can choose how to threshold it. If you want JAMM to try and automatically threshold it, use "-e auto" option. Read more about this in the FAQs on the wiki.

Example Dataset

You can use this small dataset to test if JAMM is installed correctly. Installation instructions above!

This dataset is chromosome 21, in K562 CTCF ChIP-Seq from ENCODE.

Quick Tutorial

On this link, you will find a quick tutorial to show how you can run JAMM on a real dataset.

Galaxy Wrapper

JAMM has a Galaxy wrapper which you can get from here: https://github.com/mahmoudibrahim/JAMMalaxy

The Galaxy wrapper was developed by Clemens Messerschmidt

How to Cite JAMM?

Please cite:

Ibrahim MM, Lacadie SA, Ohler U (2015). JAMM: A Peak Finder for Joint Analysis of NGS Replicates. Bioinformatics, 31(1): 48-55. doi: [10.1093/bioinformatics/btu568] (http://bioinformatics.oxfordjournals.org/content/early/2014/09/15/bioinformatics.btu568)

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Hint: While you run JAMM, you can also go on jammin...

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