Model-based Analysis of ChIP-Seq<\/a> (MACS3)<\/p>\n MACS is open source software and available to all users of the system. It is released under the BSD 3-Clause License<\/a> and all usage must adhere to that license.<\/p>\n Please ensure you cite your usage in any results and publications, as described in:<\/p>\n OR<\/p>\n We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this.<\/p>\n This will also automatically load the required version of python for you.<\/p>\n Below are legacy versions no longer supported on the CSF3. Try the Bio-informatics Helper Modulefile<\/a> if you really<\/em> have to use them.<\/p>\n Please do not run MACS on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n You may<\/em> run the following command on the login node to get some help with running MACS:<\/p>\n This will show the list of available commands (algorithms) that can be run:<\/p>\n To get help with each individual command, run:<\/p>\n Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n Submit the jobscript using: <\/p>\n where scriptname<\/em> is the name of your jobscript.<\/p>\n More info on parallel execution is available in the official documentation<\/a>.<\/p>\n Jobscript example:<\/p>\n Submit the jobscript using: <\/p>\n where scriptname<\/em> is the name of your jobscript.<\/p>\n If a newer or older version of MACS is required, it can be easily installed in a conda environment<\/a> in your home directory. Here is an example of commands to follow:<\/p>\n Then inside your jobscript, you would also need to add the following line – just after loading the miniforge module – to activate your environment:<\/p>\n None.<\/p>\n","protected":false},"excerpt":{"rendered":" Overview Model-based Analysis of ChIP-Seq (MACS3) Restrictions on use MACS is open source software and available to all users of the system. It is released under the BSD 3-Clause License and all usage must adhere to that license. Please ensure you cite your usage in any results and publications, as described in: the project’s source repository OR the project’s documentation page Set up procedure We now recommend loading modulefiles within your jobscript so that you.. Read more »<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":86,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-2962","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/2962","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=2962"}],"version-history":[{"count":15,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/2962\/revisions"}],"predecessor-version":[{"id":13047,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/2962\/revisions\/13047"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/86"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/media?parent=2962"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}Restrictions on use<\/h2>\n
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Set up procedure<\/h2>\n
\r\n# MACS3\r\nmodule load apps\/python\/macs\/3.1.0 # Python 3.14 (extensions compiled with GCC 14.2.0)\r\n\r\n# MACS2 Python3-based versions\r\nmodule load apps\/python\/macs2\/2.2.5\r\n\r\n# MACS2 Python2-based versions\r\nmodule load apps\/python\/macs2\/2.1.3.3\r\n<\/pre>\n
\r\nmodule load apps\/macs\/2.1.2\r\nmodule load apps\/macs\/2.1.1.20160309\r\nmodule load apps\/macs\/2.1.0.20150731\r\nmodule load apps\/macs\/2.1.0.20150420\r\nmodule load apps\/macs\/2.1.0\r\n<\/pre>\n
Running the application<\/h2>\n
\r\nmacs3 -h # for MACS3\r\nmacs2 -h # for MACS2\r\n<\/pre>\n
\r\ncallpeak, bdgpeakcall, bdgbroadcall, bdgcmp,\r\nbdgopt, cmbreps, bdgdiff, filterdup,\r\npredictd, pileup, randsample, refinepeak\r\ncallvar, hmmratac\r\n<\/pre>\n
\r\nmacs3 command<\/em> -h\r\n# OR\r\nmacs2 command<\/em> -h\r\n<\/pre>\n
Serial batch job submission<\/h3>\n
\r\n#!\/bin\/bash --login\r\n#SBATCH -p serial\r\n#SBATCH -t 0-6\r\n\r\n# We recommend loading modulefiles in jobscripts. Use your required version.\r\nmodule purge\r\nmodule load apps\/python\/macs\/3.1.0\r\n\r\nmacs3 command<\/em> arg1 arg2 ...<\/em> --threads $SLURM_CPUS_PER_TASK\r\n<\/pre>\n
sbatch scriptname<\/em><\/pre>\n
Parallel batch job submission<\/h3>\n
\r\n#!\/bin\/bash --login\r\n#SBATCH -p multicore_small\r\n#SBATCH -t 0-6\r\n#SBATCH -c 8\r\n\r\nmodule purge\r\nmodule load apps\/python\/macs\/3.1.0\r\n\r\nmacs3 command<\/em> arg1 arg2 ...<\/em> --threads $SLURM_CPUS_PER_TASK\r\n<\/pre>\n
sbatch scriptname<\/em><\/pre>\n
Installation in a conda environment<\/h2>\n
\r\nmodule load apps\/binapps\/conda\/miniforge3\/26.9.4-0-w-mamba \r\nconda create --name macs3_env<\/em> --strict-channel-priority macs3\r\n# Answer y (for yes) when prompted\r\nconda activate macs3_env<\/em>\r\nmacs3 -h\r\n<\/pre>\n
\r\nconda activate macs3_env<\/em>\r\n<\/pre>\n
Further info<\/h2>\n
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Updates<\/h2>\n