| With the improvement of sequencing techniques, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq) is getting popular to study genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq analysis method, we present a novel algorithm, named Model-based Analysis of ChIP-Seq (MACS), for identifying transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and MACS improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used for ChIP-Seq data alone, or with control sample with the increase of specificity. https://github.com/taoliu/MACS/ |
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/macs2
| Repository package_atlas_3_10 revision 98c017ec230d owned by iuc (prior install required) |
| Repository package_atlas_3_10 revision 98c017ec230d owned by iuc (prior install required) |
| Repository package_numpy_1_7 revision 300877695495 owned by iuc (prior install required) |
| Repository package_readline_6_2 revision 5313ca2fbce6 owned by iuc (prior install required) |
| Repository package_ncurses_5_9 revision 335ebf512407 owned by iuc (prior install required) |
| Repository package_ncurses_5_9 revision 335ebf512407 owned by iuc (prior install required) |
| Repository package_numpy_1_7 revision 300877695495 owned by iuc (prior install required) |
| Repository package_scipy_0_12 revision cfbbe183f8a7 owned by iuc (prior install required) |
| Repository package_gnu_awk_4_1_0 revision f145f856ec57 owned by iuc |
| Name | Version | Type | |
|---|---|---|---|
| R_3_0_1 | 3.0.1 | package | |
| gnu_awk | 4.1.0 | package | |
| macs2 | 2.1.0 | package | |
| numpy | 1.7.1 | package | |
| scipy | 0.12.0 | package | |
| MACS2_SCRIPT_PATH | set_environment | ||
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| Call broad peaks from bedGraph output | 2.1.0.20140616.0 | any | |
| Predict 'd' or fragment size from alignment results | 2.1.0.20140616.0 | any | |
| Randomly sample number or percentage of total reads | 2.1.0.20140616.0 | any | |
| Differential peak detection based on paired four bedgraph files | 2.1.0.20140616.0 | any | |
| Remove duplicate reads at the same position | 2.1.0.20140616.0 | any | |
| Refine peak summits and give scores measuring balance of forward- backward tags (Experimental) | 2.1.0.20140616.0 | any | |
| Call peaks from alignment results | 2.1.0.20140616.0 | any | |
| Deduct noise by comparing two signal tracks in bedGraph | 2.1.0.20140616.0 | any | |
| Call peaks from bedGraph output | 2.1.0.20140616.0 | any | |