Model-based Analysis of ChIP-Seq (MACS) is used on short reads sequencers such as Genome Analyzer (Illumina / Solexa). MACS empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size estimates, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome sequence, allowing for more sensitive and robust prediction. MACS compares favorably to existing ChIP-Seq peak-finding algorithms and can be used for ChIP-Seq with or without control samples.
MACS is written by Yong Zhang and Tao Liu from Xiaole Shirley Liu's Lab.
The environment variable(s) need to be set properly first. The easiest way to do this is by using the modules commands as in the example below.
$ module avail macs ---------------------- /usr/local/Modules/3.2.9/modulefiles -------------------------------- macs/1.4.1 macs/1.4.2 macs/2.0.10(default) $ module load macs $ module list Currently Loaded Modulefiles:
1) macs/2.0.10 $ module unload macs $ module load macs/1.4.2 $ module show macs ------------------------------------------------------------------- /usr/local/Modules/3.2.9/modulefiles/macs/2.0.10: module-whatis Sets up macs 2.0.10 prepend-path PYTHONPATH /usr/local/Python/2.7.2/lib/python2.7/site-packages prepend-path PATH /usr/local/Python/2.7.2/bin -------------------------------------------------------------------
Sample Session on Helix
macs sample file can be copied from:
/usr/local/apps/macs/FoxA1_ChIP-seq.tar.gz
Put the sample file under user's own area:
$ mkdir /data/$USER/macs/run1 $cd /data/$USER/macs/run1 $cp /usr/local/apps/macs/FoxA1_ChIP-seq.tar.gz . $tar xvfz FoxA1_ChIP-seq.tar.gz
To run macs, first do this before running macs:
$ module load macs $ macs2 callpeak -t Treatment_tags.bed -c Input_tags.bed --name test
