bed2bed_display.c:	-a	Min BED score
bed2bed_display.c:	-b	Max BED score
bed2bed_display.c:	-d|--debug	Produce Debug information\n"
bed2bed_display.c:	-f|--feature <ft>	Set Feature name <ft>\n"
bed2bed_display.c:	-h|--help	Show this Help text\n"
bed2bed_display.c:	-o|--oformat <1|2>	Set output Format (1:BED[Def] 2:BedGraph)\n"
bed2sga.c:	-c|--center	Generate a Centered SGA file\n"
bed2sga.c:	-d|--debug	Produce Debug information\n"
bed2sga.c:	-e|--extend <f1,f2,...>	Produce an extended SGA file with additional fields specified\n"
bed2sga.c:	-f|--feature <ft>	Set Feature name <ft>\n"
bed2sga.c:	-h|--help	Show this Help text\n"
bed2sga.c:	-i|--db <path>	Use <path> to locate the assembly-specific chr_NC_gi file\n"
bed2sga.c:	-r|--regional	Generate a 2-line[+/-] SGA file representing BED regions\n"
bed2sga.c:	-s|--species <spec>	Assembly <spec> (i.e hg19)\n"
bed2sga.c:	-u|--unoriented	Generate an unoriented SGA file\n"
check_bed.pl:	-f <BED file>	Specify BED file
check_bed.pl:	-s <species>	Specify species
chipcenter.c:	-c	Count Cut-off (default is %d)\n"
chipcenter.c:	-d	Print debug information\n"
chipcenter.c:	-f	feature
chipcenter.c:	-h	Show this help text\n"
chipcenter.c:	-i <dir>	Directory where the chr_size file is found\n"
chipcenter.c:	-r	New feature name (for feature replacement)\n"
chipcenter.c:	-s	shift
chipcenter.c:	-z	Set strand to zero\n"
chipcor.c:	-c	Cut-Off value for feature counts (default is %d)\n"
chipcor.c:	-d	Print debug information and check SGA file\n"
chipcor.c:	-h	Show this help text\n"
chipcor.c:	-n	Histogram Normalization (default is %d)\n"
chipcor.c:	-o	Oriented strand processing\n"
chipextract.c:	-A	feature A
chipextract.c:	-b	from
chipextract.c:	-B	feature B
chipextract.c:	-c	Cut-Off value for target feature counts (default is %d)\n"
chipextract.c:	-d	Print debug information and check SGA file\n"
chipextract.c:	-e	to
chipextract.c:	-h	Show this help text\n"
chipextract.c:	-w	width
chippart.c:	-c <cutoff>	Count Cut-off (default is %d). It must be >= 0.\n"
chippart.c:	-d	Print debug information and check SGA file\n"
chippart.c:	-f	feature
chippart.c:	-h	Show this help text\n"
chippart.c:	-p	transition penalty
chippart.c:	-s	density threshold
chippeak.c:	-c	Count Cut-off (default is %d)\n"
chippeak.c:	-d	Print debug information and check SGA file\n"
chippeak.c:	-f	feature
chippeak.c:	-h	Show this help text\n"
chippeak.c:	-i <dir>	Directory where the chr_size file is found\n"
chippeak.c:	-o	Oriented strand processing\n"
chippeak.c:	-r	Refine Peak Positions\n"
chippeak.c:	-t	threshold
chippeak.c:	-v	vicinity
chippeak.c:	-w	window
chipscore.c:	-A	feature A
chipscore.c:	-b	from
chipscore.c:	-B	feature B
chipscore.c:	-c <cutoff>	Cutoff value for feature counts (default is %d)\n"
chipscore.c:	-d	Print debug information and check SGA file\n"
chipscore.c:	-e	to
chipscore.c:	-h	Show this help text\n"
chipscore.c:	-o	Oriented strand processing\n"
chipscore.c:	-q	Report feature B tag counts as 'feature_name=<int>'\n"
chipscore.c:	-r	Reverse extraction process\n"
chipscore.c:	-t	threshold
chr_replace_sga.pl:	-d <dir>	directory where chro_idx.nstorage is to be found.
chr_replace_sga.pl:	-f <dir>	file
chr_replace_sga.pl:	-s <dir>	species
compactsga.c:	-d	Print debug information\n"
compactsga.c:	-h	Show this help text\n"
countsga.c:	-c	Count Cut-off (default is %d)\n"
countsga.c:	-d	Print debug information\n"
countsga.c:	-f	Feature specifications [name [+|-]]\n"
countsga.c:	-h	Show this help text\n"
eland2sga.pl:	-a feature
eland2sga.pl:	-f eland_file
eland2sga.pl:	-i db-dir
eland2sga.pl:	-s species
featreplace.c:	-d	Print debug information\n"
featreplace.c:	-f	feature name
featreplace.c:	-h	Show this help text\n"
filter_counts.c:	-d	Print debug information\n"
filter_counts.c:	-f	Feature defining the user-defined regions of interest (default=RMSK)\n"
filter_counts.c:	-h	Show this help text\n"
filter_counts.c:	-r	Retain Mode on\n"
fps2sga.pl:	-f|--feature <feature>	Set Feature name <feature>
fps2sga.pl:	-h|--help	Show this stuff
fps2sga.pl:	--ignore0flag	Ignore 0 flag at position 29 of the FP line,
fps2sga.pl:	-s|--species <species>	Assembly <species> (i.e hg18)
fps2sga.pl:	-x	Generate an extended SGA file with the
gff2sga.pl:	-a	feature
gff2sga.pl:	-c	Generate a Centered SGA file
gff2sga.pl:	--db <path>	Use <path> to locate Chrom Id Storable File 'chro_idx.nstorage'
gff2sga.pl:	-f|--feature <feature>	Set Feature name <feature>
gff2sga.pl:	-h|--help	Show this stuff
gff2sga.pl:	-s|--species <species>	Assembly <species> (i.e hg18)
gff2sga.pl:	-u	Generate an Unoriented SGA file
gff2sga.pl:	-u	unoriented
gff2sga.pl:	-x	Generate an extended SGA file with the
partit2bed.pl:	-b <int>	Chromosome start [def: $chr_start - entire chrom region]
partit2bed.pl:	--color <RRR,GGG,BBB>	Define the main color for the annotation track [def: $color]
partit2bed.pl:	--db <path>	Use <path> to locate Chrom Id Storable File 'chro_idx.nstorage'
partit2bed.pl:	-d|--desc <desc>	Description field of the BED header line [def: $desc]
partit2bed.pl:	-e <int>	Chromosome end [def: $chr_start - entire chrom region]
partit2bed.pl:	-h|--help	Show this stuff
partit2bed.pl:	-n <int>	Chromosome number (BED declaration lines) [def: 0 - all chromosomes]
partit2bed.pl:	-t|--track <track>	BED track name [def: $track_name]
partit2sga.pl:	-b	Chromosome start
partit2sga.pl:	-d	Description
partit2sga.pl:	--db <path>	Use <path> to locate Chrom Id Storable File 'chro_idx.nstorage'
partit2sga.pl:	-e	Chromosome end
partit2sga.pl:	-h|--help	Show this stuff
partit2sga.pl:	-n	Chromosome number
partit2sga.pl:	-t	Track name
sga2bed.c:	-b|--bk_ext <len>	Set 5p-end extension <len>(bp)\n"
sga2bed.c:	-c|--score <score>	Normalisation factor for BED score field (5th) [score=1]\n"
sga2bed.c:	-d|--debug	Produce Debug information\n"
sga2bed.c:	-e|--extend f1:F1[,f2:F2]	Set SGA optional field(s) f1(,f2,...) to BED field(s) F1,(F2,..)\n"
sga2bed.c:	-f|--fw_ext <len>	Set 3p-end extension <len>(bp)\n"
sga2bed.c:	-h|--help	Show this Help text\n"
sga2bed.c:	-i|--db <dir>	Directory where the chr_size file is found (default: CWD)\n"
sga2bed.c:	-l|--readlen <len>	Set Read length <len>(bp)\n"
sga2bed.c:	-r|--nohdr	BED format without annotation track header lines\n"
sga2bed.c:	-x|--expand	Expand SGA lines into multiple BED lines\n"
sga2fps.pl:	--db <path>	Use <path> to locate Chrom Id Storable File 'chro_idx.nstorage'
sga2fps.pl:	-f <feature>	Set <feature> field
sga2fps.pl:	-h|--help	Show this stuff
sga2fps.pl:	--set0flag	Set 0 flag at position 29 of the FP line, forcing unoriented output
sga2fps.pl:	-s|--species <species>	Assembly <species> (i.e hg18)
sga2gff.pl:	--db <path>	Use <path> to locate Chrom Id Storable File 'chro_idx.nstorage'
sga2gff.pl:	-e|--ext <ext_flag>	Use SGA 6th field to set GFF feature field
sga2gff.pl:	-h|--help	Show this stuff
sga2gff.pl:	-l|--taglen <taglen>	Set Read length <taglen>
sga2gff.pl:	-x	Expand SGA lines into multiple GFF lines
sga2wig.c:	-b|--start  <int>	Chromosome start [def: -1 (entire chromosome)]\n"
sga2wig.c:	-c|--coff   <int>	Count cut-off for the SGA input file [def=99999]\n"
sga2wig.c:	-d|--debug	Produce Debug information\n"
sga2wig.c:	-e|--end    <int>	Chromosome end [def: -1 (entire chromosome)]\n"
sga2wig.c:	-f|--norm   <int>	Normalization factor for total tag counts within step intervals [def=0]\n"
sga2wig.c:	-h|--help	Show this Help text\n"
sga2wig.c:	-i|--db <path>	Use <path> to locate the chr_NC_gi and chr_size files\n"
sga2wig.c:	-n|--chrnb  <int>	Chromosome number [def: 0 (all chromosomes)]\n"
sga2wig.c:	-o|--format <0|1>	Set Wiggle Track data format: variableStep[def=0]/fixedStep[1]\n"
sga2wig.c:	-s|--span   <int>	Wiggle Track Span(/stepInterval) parameter [def=%d]\n"
sga2wigSmooth_FS.pl:	-a	Assembly used in the SGA file
sga2wigSmooth_FS.pl:	-c	Count cut-off, defoult set to 1
sga2wigSmooth_FS.pl:	-f	Fragment size of ChIP-seq experiment. Default value 150
sga2wigSmooth_FS.pl:	-s	Span used in the WIG sile, default set to 10
wigVS2sga.pl:	--db <path>	Use <path> to locate Chrom Id Storable File 'chro_idx.nstorage'
wigVS2sga.pl:	-f|--feature <feature>	Set Feature name <feature> [def=WIG]
wigVS2sga.pl:	-h|--help	Show this stuff
wigVS2sga.pl:	-n <int>	Normalization factor for data value: it needs to be converted to INTEGER [def=1]
wigVS2sga.pl:	-s|--species <species>	Assembly <species> [def=hg19]
