Up: Component summary
Up: Component summary
Component
SPPWraps the SPP R package from http://compbio.med.harvard.edu/Supplements/ChIP-seq/ published in Kharchenko PK, Tolstorukov MY, Park PJ "Design and analysis of ChIP-seq experiments for DNA-binding proteins" Nat. Biotech. doi:10.1038/nbt.1508
| Version | 1.0 |
|---|---|
| Bundle | sequencing |
| Categories | |
| Authors | Lauri Lyly (lauri.lyly@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | R ; SPP 1.10 (R-package) |
| Source files | component.xml SPP.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| treatment | BinaryFile | Mandatory | Sample CSV file, with fields: chromosome name, region middle position, strand (either 1 for forward or 2 for reverse) |
| control | BinaryFile | Mandatory | Control CSV file with similar format as treatment file. |
Outputs| Name | Type | Description |
|---|---|---|
| peaks | CSV | Called peaks regions ... |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| bin | int | 5 | bin tags within the specified number of basepairs to speed up calculation |
| fdr | float | 0.01 | Desired FDR. |
| srange_max | int | 500 | |
| srange_min | int | 50 |