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
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