Getting Started

The FLUX CAPACITOR is run with the command

./flux capacitor [-r|-ref] <file.gtf> [-s|-sra] <file.bed> [options]

with the following parameters

REQUIRED ARGUMENTS
-r|--ref <file>	specify REFerence annotation (GTF format)
-s|--sra <file>	specify the Short Read Alignment file (BED format)

SYSTEM-DEPENDENT PARAMETERS
-i|--lib <file>	path to the native libraries if I cannot guess it

ALGORITHM PARAMETERS
[-n|--noise]	the fraction of permitted noise level [0.0,1.0]

OUTPUT OPTIONS
[-f|--force]	F for force, suppresses communication on stderr
[-o|--out <file>]	send output to file (DEFAULT stdout)
[-l|--locus]	additionally output elements of the locus (i.e., features 'locus' and 'transcript')
[-g|--graph]	outputs graph information, i.e., GFF features 'fragments' and 'junctions'

Examples

A test program run can with the demonstration files in the distribution:

$ ./bin/flux.sh -r demo/hg18_knownGenes_fromUCSC081019_sorted.gtf -s demo/seq-150_200.bed > output.gtf

Pipeline mode: efficiently written to a file, silence on stdout and stderr:

$ ./bin/flux.sh -s demo/seq-150_200.bed -r demo/hg18_knownGenes_fromUCSC081019_sorted.gtf -fo myOutput.gtf

Extended output including information about transcripts, loci and the splicing graphs and higher stringency concerning the noise model:

$ ./bin/flux.sh -lgn 0.1 --ref demo/hg18_knownGenes_fromUCSC081019_sorted.gtf --sra demo/seq-150_200.bed

For additional information refer to the FAQ or visit the FLUX CAPACITOR forum