--add-annotations <Boolean> |
Add peak annotations to reference sequences in mappings (default: true) |
--analyze-separately <Boolean> |
Calculate individual false discovery rates for each contig (default: false) |
--create-fdr-graph <Boolean> |
Create a graph showing empirical distribution of window read count and the estimated negative binomial distribution (default: false) |
--create-fdr-table <Boolean> |
Create a table of observed and expected read counts and estimated FDR values (default: false) |
--create-peak-table <Boolean> |
Create a table of estimated ChIP-seq binding regions (default: true) |
-d, --destination <ClcUrl> |
Destination file or folder on server. If not specified the folder of the first input object will be used. |
--filter-ratio |
|
Double: 0.0 <= x <= 1.0 |
Maximum forward / reverse normalized difference (default: 0.4) |
--filter-read-orientation <Boolean> |
Remove peaks if the absolute value of the normalized difference between forward and reverse read counts is below the user specified value (default: false) |
--filter-wilcoxon <Boolean> |
Remove peaks if the test probability of the Wilcoxon rank sum test of identical forward/reverse read location (default: true) |
--filter-wilcoxon-p-value |
|
Double: 0.0 <= x <= 1.0 |
Maximum allowed probability of identical distributions of forward and reverse reads (default: 1.0E-4) |
-i, --input <ClcUrl> |
Input data on server |
--log <Boolean> |
Enable creation of algo log file. (default: true) |
--max-fdr |
|
Integer: 0 <= x <= 100 |
Windows with a higher rate of false discovery will be discarded (default: 5) |
--peak-refinement <Boolean> |
Refine binding site border using the distibution of forward and reverse reads (default: true) |
--shift-reads <Boolean> |
When selected, all reads are shifted towards the 3' end prior to peak detection. This will increase sensitivity of peak detection. (default: true) |
--shift-reads-fragment-length |
|
Integer: 0 <= x <= 10000 |
The length of sequencing fragments. Reads will be shifted a distance of this value / 2. (default: 200) |
--use-control <Boolean> |
Use control (default: false) |
--use-control-mapping <ClcUrl> |
When using control sample, specify the mapping file on server |
--window-shifted |
|
Integer: 0 <= x <= 10000 |
Set size of scanning window (default: 250) |