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Mahmoud Ibrahim edited this page Feb 21, 2020 · 13 revisions

Welcome to the JAMM wiki! The Wiki contains some important documentation and tips on how to use JAMM.

First things first, you will need to get the latest JAMM release from this page. Then you should install JAMM on your machine, this page will tell you how. Before you run JAMM, check out the Usage page which explains all the command line parameters that you can set and if you're still having problems, you can go through a quick tutorial and look at parameter recommendations.

While you're running JAMM read some Frequently Asked Questions. After JAMM is done, you will probably be satisfied with the results :) but we do appreciate you emailing us if you have questions or you run into problems (we really do like getting emails about JAMM, I'm not just saying that).

Finally, please do check out our tips on pre-processing ATAC-seq for calling peaks with JAMM if you're analyzing ATAC-seq data.

News and Updates

  • Feb 21 2020: JAMM will be updated incrementally over the next few months under version 1.0.8.x to improve performance and speed. These updates are stable, synced directly to the master repository and released as pre-releases. However, they may change output somewhat significantly, so use at your risk. The most recent stable and tested version is v1.0.7.6 which you can get from the releases page.

  • May 17 2019: New version of JAMM released (v1.0.7rev6). This version features some small changes to input checks.

  • July 14 2016: New version of JAMM released (v1.0.7rev5). This version adds -T parameter for custom temporary directory (thanks to @amathelier) as well as streamlined code and fixed bugs in peakfinder.r.

  • 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.

  • Sep 25 2015: Please note that v1.0.7rev2 has a bug that might cause paired-end analysis mode to crash. If you want to set -t paired, please use v1.0.7rev1 until a fix is released. On a different note, there is now a tutorial on the wiki on how to analyze ATAC-seq data.

  • Jul 30 2015: New version of JAMM released (v1.0.7rev2). This version has some minor bug fixes and some cryptic errors replaced by user-friendly messages.

  • Feb 18 2015: New version of JAMM released (v1.0.7rev1). This version introduces clustering model initialization options among other things, optional PCR duplicates filtering and reports the seed used for all randomization/sampling steps.

  • Jan 14 2015: New questions and answers have been added to the FAQs wiki page. Why does JAMM output a large number of peaks? What is the "filtered" list?...Those questions and more are answered in the FAQs wiki page!

  • Dec 06 2014: New version of JAMM released (v1.0.6rev3). This version fixes a bug related to bash localization that affects peak score sorting for some users. You can read more in the changelog.

  • Nov 25 2014: New version of JAMM released (v1.0.6rev2). This version fixes bugs in the previous released version JAMMv1.0.6rev1, that cause paired-end option to not function.

  • Nov 11 2014: New version of JAMM released (v1.0.6rev1). This version has two main changes: NO dependencies on "sqldf" R package, and optional window fold enrichment cutoff to reduce running time and get only more highly confident peaks.

  • Nov 11 2014: After a recent R update, certain versions of some R packages are not compatible with certain versions of the "sqldf" R package. This affects all JAMM versions from v1.0.4 until v1.0.6. Starting v1.0.6rev1, JAMM has NO dependencies on "sqldf" package.

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