Capacitor Usage

usage: flux

Parameter	Parameter	Default	Description
-cb,--costBounds	Float,Float		cost boundaries in the form of $\mathit{factor_{min},factor_{max}}$ where $\mathit{factor_{min}}$ is the factor to determine the minimum (and $\mathit{factor_{max}}$ correspondingly the factor for obtaining the maximum) number of reads that can be predicted with respect to the originally observed reads. See the page about the objective function for details about the cost boundaries.
-cm,--costModel	lin|log[Float]	log	cost model, either linear or logarithmical. In the case of linear costs, the a slope different than 1 can be controlled by the optional Float argument.
-cs,--costSplit	Integer	5	the number of linear segments that approximate the function underlying the cost model
-d,--decompose			perform the flow network decomposition. Important: in Capacitor 20090718 there is no output produced if this option is not applied.
-f,--force			suppresses communication on stderr
-g,--graph			outputs graph information, i.e., GTF features fragment and junction
-i,--lib	String		path to the lpsolve native libraries
-l,--locus			additionally output elements of the locus, i.e., GTF features locus and transcript
-m,--map			perform the mapping (i.e., "profiling") step. Important: in Capacitor 20090718 this step alone does not produce any output. If applied, it collects information about the read distribution, otherwise the assumption is uniformally distributed reads.
-o,--out	String	stdout	write output to a file with the given path
-p,--pair	Integer,Integer}		activate paired-end, specify insert size range by $\mathit{size_{min},size_{max}}$
-r,--ref	String		Mandatory: file with the reference annotation (GTF format)
-s,--sra	String		Mandatory: file with the short read alignment (BED format)
-t,--strand			activate strand information