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README
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* Attention
This my personal code repository. I haven't tested them fully. So I can't guarantee they works...
* Ancient README
* WebApp list:
1. CistromeDB
The CistromeDB website based on Django framework. Check
CistromeDB/INSTALL.txt for detail.
* Exectuables list:
1. motif_enrich.py
Usage: motif_enrich.py [options]
Calculate the motif enrichment measured in foldchange and p-value for one BED
file and one reference BED file
Options:
--version show program's version number and exit
-h, --help Show this help message and exit.
-s SPECIES, --species=SPECIES
species, must be "mm8" or "hg18"
-i IFILE, --ifile=IFILE
input BED file, e.g. the ChIP regions
-r RFILE, --rfile=RFILE
input reference BED file, e.g. the tiled regions.
[optional] if not set, use the whole genome as
reference
-c CUTOFF, --cutoff=CUTOFF
cutoff for the motif scan score
-d IDIR, --idir=IDIR input directory for binary Motif Scan Results files
-a, --all If set, also show the depleted motifs. Default, not
show
--minfc=MINFC minimum foldchange for motif enrichment, default:0
--maxp=MAXP maximum p-value for motif enrichment, default:1
--minpercent=MINPERCENT
minimum percentage of input BED regions containing
motif, default:5
--maxpercent=MAXPERCENT
maximum percentage of input BED regions containing
motif, default:300
--verbose=VERBOSE Name of a directory. if set, save verbose information
in the direcotry.
-o OFILE, --ofile=OFILE
output file
2. ceas.py
Usage: ceas.py [options]
CEAS -- Cis-regulatory Element Annotation System
Options:
--version show program's version number and exit
-h, --help Show this help message and exit.
--chip-res=CHIP_RES ChIP resolution, default: 600 bp
--bg-res=BG_RES Genome BG resolution, default: 100 bp
--promoter=PROMOTER Promoter range size, default: 3000 bp
--bipromoter=BIPROMOTER
Bidirectional-promoter range size, default: 5000 bp
--downstream=DOWNSTREAM
Downstream range size, default: 3000 bp
--nopf No profiling is run and the options regarding
profiiling will not be effective if this switch is set
--rel-dist=REL_DIST Relative distance to TSS/TTS for gene profiling,
default: 3000 bp
--metagene-size=METAGENE_SIZE
Metagene size, default: 3000 bp
--pf-res=PF_RES Profiling resolution, default: 50 bp
--gn-groups=GN_GROUPS
Gene-group file names (eg, top10.txt,bottom10.txt),
default: all genes
--gn-group-names=GN_NAMES
Gene-group names for profiling (eg, top 10%,bottom
10%), default: None
-a, --alt-gn-name 'name2' in refGene table is used if set. This flag is
meaningful only if --gn-groups is set.
-i IFILE, --ifile=IFILE
input BED file, e.g. the ChIP regions
-w WFILE, --wfile=WFILE
input wiggle file.
-n NCBED, --ncbed=NCBED
noncoding region BED file, default: None
-g GDB, --gene-db=GDB
Gene annotation database file from Cistrome website
--gt=GT optional genome table. default: None
-o OFILE, --ofile=OFILE
output R script. default: stdout
--verbose=VERBOSE Name of a directory. if set, save verbose information
in the direcotry.
3. qc_chIP.py
Usage: qc_chIP.py [options]
QC for two replicates of ChIP-chip experiment. Do both peak level and
probe level calculations.
Options:
--version show program's version number and exit
-h, --help Show this help message and exit.
-p PEAK1, --peak1=PEAK1
peak file in xls format for #1 replicate
-q PEAK2, --peak2=PEAK2
peak file in xls format for #2 replicate
-x WIG1, --wig1=WIG1 wiggle file for #1 replicate
-y WIG2, --wig2=WIG2 wiggle file for #2 replicate
-r RFILE, --rfile=RFILE
R output file
-f FORMAT, --format=FORMAT
ma2c, mat or macs, default: ma2c
-s STEP, --step=STEP number of steps to calculate cor based on some score
ranges, default: 5
4. qc_chIP2.py
Usage: qc_chIP2.py [options]
QC for two replicates of ChIP-chip experiment. Only for naive overall
probe level calculation.
Options:
--version show program's version number and exit
-h, --help Show this help message and exit.
-x WIG1, --wig1=WIG1 wiggle file for #1 replicate
-y WIG2, --wig2=WIG2 wiggle file for #2 replicate
-r RFILE, --rfile=RFILE
R output file. If not set, do not save R file.
-s STEP, --step=STEP probe step, default: 100
-f FORMAT, --format=FORMAT
ma2c, mat or macs, default: ma2c
5. count_probes_in_peaks.py
Usage: count_probes_in_peaks.py [options]
Summarize ChIP-chip experiment. Calculate how many probes are included
in peak regions.
Options:
--version show program's version number and exit
-h, --help Show this help message and exit.
-p PEAK1, --peak1=PEAK1
peak file in xls format for #1 replicate
-x WIG1, --wig1=WIG1 wiggle file for #1 replicate
-o OFILE, --ofile=OFILE
output file
-f FORMAT, --format=FORMAT
ma2c, mat or macs, default: ma2c
6. count_probes_in_ranges.py
Usage: count_probes_in_ranges.py [options]
Summarize ChIP-chip experiment. Calculate how many probes fall into
certain score ranges '(-inf,-1],(-1,0],(0,+1],(+1,+inf)'.
Options:
--version show program's version number and exit
-h, --help Show this help message and exit.
-x WIG1, --wig1=WIG1 wiggle file for #1 replicate
-o OFILE, --ofile=OFILE
output file
7. xyz2image.py
Restore the microarray image.
need 1 parameter: xyz2image.py <X-Y-Value-file>
X-Y-Value-file is a tab-delimited file with 1st column as
X-corrdinates, 2nd column as Y, and 3rd column as log-ratio value