MACS
Overview
Model-based Analysis of ChIP-Seq (MACS2)
Various versions are installed, 2.2.5 (using python 3) being the latest:
- 2.1.0.20150731
- 2.1.0.20150420
- 2.1.0
- 2.1.1.20160309
- 2.1.2
- 2.1.3.3
- 2.2.5
Restrictions on use
MACS2 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. The reference is:
“Zhang et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biol (2008) vol. 9 (9) pp. R137″.
Set up procedure
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. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.
# Python 3 versions module load apps/python/macs2/2.2.5 # Python 2 versions module load apps/python/macs2/2.1.3.3 module load apps/macs/2.1.2 # Note the change in modulefile naming scheme module load apps/macs/2.1.1.20160309 module load apps/macs/2.1.0.20150731 module load apps/macs/2.1.0.20150420 module load apps/macs/2.1.0
This will also automatically load the required version of python for you.
Running the application
Please do not run MACS2 on the login node. Jobs should be submitted to the compute nodes via batch.
You may run the following command on the login node to get some help with running MACS2:
macs2 -h
This will show the list of available commands (algorithms) that can be run:
callpeak, bdgpeakcall, bdgbroadcall, bdgcmp, bdgopt, cmbreps, bdgdiff, filterdup, predictd, pileup, randsample, refinepeak
To get help with each individual command, run:
macs2 command -h
Serial batch job submission
Create a batch submission script (which will load the modulefile in the jobscript), for example:
#!/bin/bash --login #$ -cwd # Job will run from the current directory # NO -V line - we load modulefiles in the jobscript # We recommend loading modulefiles in jobscripts. Use your requried version. module load apps/python/macs2/2.2.5 macs2 command arg1 arg2 ...
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Further info
Updates
None.