chip_seq

--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 <ClcServerObjectUrl> 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 <ClcObjectUrl> 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 <ClcObjectUrl> When using control sample, specify the mapping file on server
--window-shifted
Integer: 0 <= x <= 10000 Set size of scanning window (default: 250)