Study protein-DNA interaction using ChIP-Seq data. TThe Genome Positioning System (GPS) is a software tool to study protein-DNA interaction using ChIP-Seq data. GPS builds a probabilistic mixture model to predict the most likely positions of binding events at single-base resolution.

GPS has 3 main features:
1. Achieve high spatial resolution on predicting binding events
2. Resolve closely spaced (less than 500bp) events that appear as a single cluster of reads
3. Process multiple dataset simultaneously to align common events across distinct experiments

GPS Usage
Required parameters:
--d <read distribution file>
--s <size of mappable genome in bp>
--exptX <aligned reads file for expt (X is condition name)>
--ctrlX <aligned reads file for ctrl (X is condition name)>
Optional parameters:
--f <read file format, BED/BOWTIE/ELAND/NOVO (default BED)>
--g <genome info file with chr name/length pairs>
--r <max rounds to refine read distribution (default=3)>
--a <minimum alpha value for sparse prior (default=6)>
--q <significance level for q-value, specify as -log10(q-value), (default 2, q-value=0.01)>
--t <maximum number of threads to run GPS in paralell, (default=#CPU)>
--out <output file base name>
Optional flags:
--fa <use a fixed user-specified alpha value for all the regions>
--help <print help information and exit>

Output format:
The output file contains eight fields in a tab-delimited file:
- Binding event coordinate
- IP read count
- Control read count
- Fold enrichment (IP/Control)
- P-value
- Q-value (multiple hypothesis corrected)
- Shape deviation from the empirical read distribution (log10(KL))
- Shape deviation between IP vs Control (log10(KL))

Requirements:
* Java

The license of this software is Freeware, you can free download and free use this calculator software.