Difference between revisions of "MACS"
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WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used) | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used) | ||
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Revision as of 16:32, 10 August 2012
Description
Next generation parallel sequencing technologies made chromatin immunoprecipitation followed by sequencing (ChIP-Seq) a popular strategy to study genome-wide protein-DNA interactions, while creating challenges for analysis algorithms. We present Model-based Analysis of ChIP-Seq (MACS) 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, is publicly available open source, and can be used for ChIP-Seq with or without control samples. Upstream documentation for macs.
Available Versions
- 1.4.1 (EL5)
- 1.4.2 (EL6)
Execution Environment and Modules
To use macs with the environment modules system at HPC the following commands are available:
Get module information for macs:
$module spider macs
Load the default application module:
$module load macs
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_MACS_DIR - directory where macs is located.
- HPC_MACS_BIN - Executable directory
Citation
If you publish research that uses macs you have to cite it as follows: Zhang et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biol (2008) vol. 9 (9) pp. R137