Command Line Menus
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** File Splitter: Jan 2005 bdtnp.lbl.gov **
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Splits a big text file into smaller files given a maximum number of lines.
Required Parameters:
-f Full path file name for the text file.
-n Maximum number of lines to place in each split file.
Example: java -Xmx256M FileSplitter -f /affy/bpmap.txt -n 50000
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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** BPMapOligoBlastFilter: Jan 2005 bdtnp.lbl.gov **
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BOBF takes an Affymetrix text bpmap file and BLASTs each oligo against a BLAST
database. Use formatdb on a complete genome.fasta file to create the database.
BOBF writes three files, one that assigns new coordinates to the oligo and replaces the
ori column with the number of 1bp mismatches and exact matches. A second file is
written containing oligos with only one exact match in the genome, the ori column is
replaced with the number of 1bp mismatches. The third contains oligos with no exact
match to the genome. The number of 1bp mismatches is assigned to the ori column.
This combo program is quite slow, 0.45sec
per oligo, so break up your bpmap file into separate files using the FileSplitter
program and farm the jobs out to a cluster. After processing, combine the files using
FileJoiner and sort using the BPMapSort program. If you don't care about 1bp mismatches
use MUMMER, it should take about an hour.
Required Parameters:
-b Full path file name for text bpmap file.
-d Full path file name for BLAST database.
-s Full path file name for the blastall program.
Example: java -Xmx256M BPMapOligoBlastFilter -b /affy/bpmap1 -s /ncbi/bin/blastall
-d /seq/dmel/whole_genome.fasta
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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** File Joiner: Feb 2005 bdtnp.lbl.gov **
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Joins text files into a single file, avoiding line concatenations. This is a problem
with using 'cat * > combine.txt'. Removes empty lines.
Required Parameters:
-f Full path name for the directory containing the text files.
Example: java FileJoiner -f /affy/SplitFiles/
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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** Mummer Filter: Sept 2005 bdtnp.lbl.gov **
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MF uses MUMMER to split a ProbeExporter bpmap-ish text output file into three: those
oligos with one, multiple, or no exact matches to a genome. A text version bpmap file
is created for the exact match set using the genome coordinates. Be sure to use the
BPMapSort application to resort your remapped bpmap!
*** WARNING, THE MISMATCH COORDINATES ARE ASSUMED TO BE pmX, pmY+1. THIS IS THE CASE
FOR PRE-7G SCANNED IMAGES. USE THE -n FLAG ACCORDINGLY****
Parameters:
-p Full path file name for the ProbeExporter bpmap-ish text output file.
-g Full path file or directory name containing (multi) fasta genome file(s).
-m Full path file name for the mummer application.
-n Filtering a new 7G or later ProbeExporter bpmap, default is old, pre-7G.
Example: java -Xmx500M MummerFilter -p /affy/bpmap.txt -g/affy/human/NCBIv33/
-m /Seqprgs/MUMmer3.15/mummer
You may need to increase the heap size of the java virtual machine using the -Xmx
flag. Adjust accordingly in response to out of memory errors and the available
resources. Use a machine with >2GB of ram, otherwise it will run rather slowly.
Questions, comments, suggestions? Contact superfly@lbl.gov.
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** BPMap Sort: Jan 2005 bdtnp.lbl.gov **
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Sorts a text bpmap file based on chromosome and oligo start positions.
Required Parameters:
-f Full path file name for the text bpmap file.
Example: java -Xmx500M BPMapSort -f /affy/bpmap.txt
You may need to increase the heap size of the java virtual machine using the -Xmx
flag. Adjust accordingly in response to out of memory errors and the available
resources. Use a machine with >2GB of ram, otherwise it may run rather slowly.
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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** BPMap Processor: Jan 2005 bdtnp.lbl.gov **
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The BPMapProcessor takes a bpmap file, throws out internal duplicates, notes unique
oligos spotted multiple times on the array (for subsequent averaging), creates sets of
oligos (Windows) to be used in statistical analysis, and splits the bpmap file into
separate chromosomes. If the bpmap file was blast filtered using the
BPMapOligoBlastFilter program (recommended), the number of 1bp mismatches will be
processed. A directory called 'BPMapFiles' will be created containing a variety of
output files for use by other TiMAT programs. Save it!
Windowing Parameters:
-w The maximum length for a Window in bp, default 675.
-o The minimum number of oligos in each Window, default 10.
-f Full path file name for the text bpmap file, required.
Example: java -Xmx1000M BPMapProcessor -f /affy/bpmap.txt -w 1000 -o 15
You may need to increase the heap size of the java virtual machine using the -Xmx
flag. Adjust accordingly in response to out of memory errors and the available
resources. Use a machine with >2GB of ram, otherwise it will run rather slowly.
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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** Virtual Cel: August 2005 bdtnp.lbl.gov **
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VC builds virtual chips from text cel files and saves each as a PNG image file.
Examine these images for inconsistencies that need to be masked using the Cel Masker
application. Use the following options when running VC:
-c Full path file name for the directory contain the text version cel files.
-r The number of rows on the chip, defaults to 2560.
-m Maximum intensity value to color scale, defaults to 20000.
Example: java -Xmx256M VirtualCel -c /affy/chips/
You will need to increase the heap size of the java virtual machine using the -Xmx
flag. Adjust accordingly in response to out of memory errors and the available
resources.
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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** Cel Masker: August 2005 bdtnp.lbl.gov **
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CM builds and displays a virtual chip from a text version cel file. Problem areas on
the chip can be circled and assigned zero values which are subsequently ignored by
TiMAT. Use the following options when running CP:
-c Full path file name for a text version cel file.
-r The number of rows on the chip, defaults to 2560.
-m Maximum intensity value to color scale, defaults to 20000.
Mouse click once and drag to create a selection ellipse.
Use the arrow keys for fine adjustment.
Use shift+ arrow keys to modify the ellipse.
Double click the mouse to set the ellipse and create another.
Use the i or o keys to zoom in and out.
Press the m key to apply the masks and redraw the image.
Press the q key to apply the masks and write the modified cel file to disk.
Example: java -Xmx256M CelMasker -c /affy/badChip.cel
You will need to increase the heap size of the java virtual machine using the -Xmx
flag. Adjust accordingly in response to out of memory errors and the available
resources.
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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** Cel Mapper: Feb 2005 bdtnp.lbl.gov **
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CM will substitute coordinates in a bpmap file for actual intensity values from a .cel
file and write the .celInt pseudo bpmap file to disk. Column order: oligo sequence,
t/f or the number of 1bp mismatches, chromosome, start position, PM intensity, MM
intensity.
Use the following options when running CM:
-b Full path name for the text bpmap file (required).
-c Full path file name for the '.cel' file, if a directory is specified, all '.cel'
files will be processed (required).
-r The number of rows/ columns on the array, default is 2560 (optional).
-s Add statistics for each oligo, nearest nbr Tm and %GC, to bpmap line, default is no.
Example: java -Xmx500M CelMapper -b /affy/antisense.bpmap -c /affy/Cels/
You will need to increase the heap size of the java virtual machine using the -Xmx
flag. Adjust accordingly in response to out of memory errors and the available
resources. Use a machine with >2GB of ram, otherwise it will run rather slowly.
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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** Cel Processor: Aug 2005 bdtnp.lbl.gov **
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CP bpmaps, quantile normalizes, and median scales raw intensity values from
.cel files. Group files using different directories (ie all the treatment .cel
files in one directory, all the control IgG .cel files in another).
Use the following options when running CP:
-b Full path directory name for the 'BPMapFiles' generated by the BPMapProcessor
(required).
-d One or more full path directory names, comma delimited, no spaces, containing .cel
files (required).
-u Use the Mis Match data, default is no.
-s Calculate and print statistics on each .cel file, default is no.
-q Skip quantile normalization, default is to perform QN.
-t Trim outlier intensities, default is to not trim.
-c Raw intensity outlier cutoff, everything above will be replaced, defaults to 3000.
-r Outlier replacement value, defaults to 0. Zero values are considered masked and
are ignored in all stages of normalization and testing.
-m The target median value for scaling, 0 skips scaling, default is 50.
-n The number of rows/ columns on the array, default is 2560 (D.mel).
Example: java -Xmx1500M CelProcessor -b /affy/BPMapFiles/ -d /affy/tCels,/affy/cCels
-u -s -n 2600 -m 100
You will need to increase the heap size of the java virtual machine using the -Xmx
flag. Adjust accordingly in response to out of memory errors and the available
resources. Use a machine with >2GB of ram, otherwise it will run rather slowly.
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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** Scatter Plot: Aug 2005 bdtnp.lbl.gov **
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To draw a simple scatter plot and calculate a Pearson correlation coefficient for two
serialized int
wish to skip zero values in the analysis, type 'skip' after the second file name.
Example: java -Xmx750M ScatterPlot /my/int/array1 /my/int/array2 skip
Although this program is built to handle large arrays, you may need to increase the
java virtual machine's heap size with the -Xmx500M flag. Adjust accordingly in
response to out of memory errors and the available resources.
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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** Sum Intensity Test: Aug 2005 bdtnp.lbl.gov **
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SIT performs a Wilcoxon Rank Sum test, trimmed mean ratio, log2 ratio, and relative
difference tests on processed cel files (.celp) using the following parameters:
-b The full path 'BPMapFiles' directory name generated by the BPMapProcessor program
-r The full path file name to use in saving the results
-t The full path directory name containing the serialized float
-c The full path directory name containing the serialized flaot
-i Include zero intensity values in the analysis (required if you PM-MM transformed
your data!), default is to ignore them
-l Length of the oligos, defaults to 25
-s Skip Wilcoxon Rank Sum test
Example: java -Xmx1500M SumIntensityTest -b /affy/BPMapFiles -r /affy/res/zeste.res
-t /affy/tCels -c /affy/cCels
Windows with a sum >0, ratio >1, log ratio >0, and rel diff >0 will be saved to disk.
'.sgr' files are produced for import into Affy's IGB for each of the tests
with the score assigned to the center position in the window.
You may need to increase the heap size of the java virtual machine using the -Xmx
flag. Adjust accordingly in response to out of memory errors and the available
resources. Use a machine with >2GB of ram, otherwise it will run rather slowly.
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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** Skeptical Sum Intensity Test: Aug 2005 bdtnp.lbl.gov **
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SSIT performs a Wilcoxon Rank Sum, relative difference, ratio, and log2 ratio tests on
processed cel files (.celp) using the following parameters:
-b The full path 'BPMapFiles' directory name generated by the BPMapProcessor program
-r The full path file name to use in saving the results
-t The full path directory name containing the serialized float
-c The full path directory name containing the serialized flaot
-i Include zero intensity values in the analysis, default is to ignore them
-l Length of the oligos, defaults to 25
-s Skip Wilcoxon Rank Sum test
Example: java -Xmx1500M SkepticalSumIntensityTest -b /affy/BPMapFiles -r /affy/z.res
-t /affy/tCels -c /affy/cCels
For each window, pairwise comparisons are made between each treatment and control
float
scores are identified.
Windows with scores > 0 or 1 are saved to disk as a serialized Window
.sgr files are produced for each test for import into Affy's IGB with scores centered
in each window.
You may need to increase the heap size of the java virtual machine using the -Xmx
flag. Adjust accordingly in response to out of memory errors and the available
resources. Use a machine with >2GB of ram, otherwise it may run rather slowly.
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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** Interval Maker: Aug 2005 bdtnp.lbl.gov **
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IM combines Windows into larger Intervals given minimal scores and a maximum gap.
Options:
-s Minimal statistical test score, a -10Log10(p-value), defaults to 0.
-i Minimal intensity score, defaults to 0.
-r Use relative difference scores, defaults to natural ratios.
-l Use log2 ratio scores.
-e Joint windows that pass either statistical or intensity score, default requires
passing both.
-g Maximum allowable bp gap, use negative values to force overlap, defaults to 0
-o Length of oligos on array, defaults to 25
-m Maximum statistical score, defaults to 90
-f Full path file name for the Window
all files will be processed.
Example: java -Xmx500M IntervalMaker -f /affy/res/zeste.res -r -i 1.5 -g -200
The -Xmx flag increases the allowable heap size for the java virtual machine. Adjust
accordingly in response to out of memory errors and the available resources.
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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** Window Scanner: Aug 2005 bdtnp.lbl.gov **
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WS counts the number of windows that pass a range of trimmed mean ratio or relative
difference cutoffs. Use this info to calculate false discovery rates.
-b Beginning score, defaults to 1.0
-e Ending score, defaults to 2.0
-i Ratio increment, defaults to 0.01
-r Use Relative Difference, defaults to natural ratio
-l Use Log2 Ratio score
-s Use statistical score
-t Make Intervals instead of scoring windows, defaults to using ratio scores.
-m Max gap for collapsing windows when scanning intervals, defaults to 0
-f Full path file name for the Window
all files will be processed.
Example: java -Xmx500M WindowScanner -f /affy/res/zeste.res -r
The -Xmx flag increases the allowable heap size for the java virtual machine. Adjust
accordingly in response to out of memory errors and the available resources.
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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** Load Interval Oligo Info: June 2005 bdtnp.lbl.gov **
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LIOI fetches oligo intensities, start positions, and their sequence for a given
array of intervals using the following parameters:
-b The full path 'BPMapFiles' directory name generated by the BPMapProcessor program
-s The full path directory name containing the split genomic fasta files.
-t The full path directory name containing the serialized float
-c The full path directory name containing the serialized float
-i The full path Interval
-l Length of the oligos on the microarray, default is 25.
Example: java -Xmx256M LoadIntervalOligoInfo -b /affy/BPMapFiles -s /seq/dmel/
-t /affy/tCels -c /affy/cCels
The -Xmx flag increases the allowable heap size for the Java Virtual Machine. Adjust
accordingly in response to out of memory errors and the available resources. Use a
computer with >2GB of RAM or be prepared to wait. Disk memory is very slow.
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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** Score Intervals: Jan 2005 bdtnp.lbl.gov **
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SI scores serialized Interval
binding sites. Use the following options:
-f Full path file name for the Interval
within will be processed. (Required)
-g The full path directory name to the split genomic sequences (i.e. chr2L.fasta,
chr3R.fasta...). The file prefix names should match the chromosome names in the
Intervals (ie chr2L, chr3R...). (Required)
-t Full path file name for the fasta file containing aligned trimmed examples of
transcription factor binding sites. A log likelihood position specific
probability matrix will be generated from these sequences and used to scan all
the Intervals for hits to the matrix.
-s Score cut off for the matrix. Defaults to the score of the lowest scoring sequence
used in making the LLPSPM.
-w A window size in bp for calculating the maximum binding cluster, defaults to 350bp
-i Score the best average intensity window instead of the full interval.
Example: java ScoreIntervals -f /my/affy/intervals/ -g /my/affy/DmelSeqs/ -t /my/affy/
zeste.fasta -s 4.9 -w 375 -i
Depending on the size of the Interval
size of the java virtual machine using the -Xmx500M flag. Adjust accordingly in
response to out of memory errors and the available resources.
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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** Score Chromosomes: Jan 2005 bdtnp.lbl.gov **
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SC scores chromosomes for the presence of transcription factor binding sites. Use the
following options:
-g The full path directory name to the split genomic sequences (i.e. chr2L.fasta,
chr3R.fasta...), FASTA format.
-t Full path file name for the FASTA file containing aligned trimmed examples of
transcription factor binding sites. A log likelihood position specific
probability matrix will be generated from these sequences and used to scan the
chromosomes for hits to the matrix.
-s Score cut off for the matrix. Defaults to the score of the lowest scoring sequence
used in making the LLPSPM.
Example: java -Xmx500M ScoreChromosomes -g /my/affy/DmelSeqs/ -t /my/affy/zeste.fasta
-s 4.9
You may need to increase the heap size of the java virtual machine using the -Xmx500M
flag. Adjust accordingly in response to out of memory errors and the available
resources.
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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** Score Sequences: Jan 2005 bdtnp.lbl.gov **
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SS scores sequences for the presence of transcription factor binding sites. Use the
following options:
-g The full path FASTA formatted file name for the sequence(s) to scan.
-t Full path file name for the FASTA file containing aligned trimmed examples of
transcription factor binding sites. A log likelihood position specific
probability matrix will be generated from these sequences and used to scan the
sequences for hits to the matrix.
Example: java -Xmx500M ScoreSequences -g /my/affy/DmelSeqs.fasta -t
/my/affy/zeste.fasta
You may need to increase the heap size of the java virtual machine using the -Xmx500M
flag. Adjust accordingly in response to out of memory errors and the available
resources.
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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** Find Sub Binding Regions: May 2005 **
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FSBR takes Interval
the highest scoring sub window based on their intensity score (ratio or difference,
median or mean). FSBR also picks binding peaks using smoothed intensity
values (trimmed mean sliding window of 230bp) .
Parameters:
-i The full path file name for a serialize Interval
directory, and all the Interval files within will be processed.
-f Use intensity difference, defaults to ratio.
-a Use mean, defaults to median.
-w Window size, default is 350bp.
-s Window size for smoothing intensity scores, default is 230bp.
-m Max number of binding peaks to find, defaults to 4
-c Minimum binding peak ratio score, defaults to 1.5
-n Minimum number of oligos required in sub window, default is 7.
Example: java -Xmx256M FindSubBindingRegions -i /affy/Intervals/ -w 300 -n 4
The -Xmx flag increases the allowable heap size for the Java Virtual Machine. Adjust
accordingly in response to out of memory errors and the available resources. Use a
computer with >2GB of RAM or be prepared to wait. Disk memory is very slow.
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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** Interval Filter: June 2005 bdtnp.lbl.gov **
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IF filters Interval
off(s). The reported number of cut intervals is sequential and may not reflect the
total number that would fail each particular test when multiple filtering.
-a Filter by the trimmed mean relative difference of the Best Intensity Window (BIW)
-b Filter by the trimmed mean ratio of the BIW (minimum)
-c Filter by the median intensity difference of the sub window (minimum)
-d Filter by the median ratio of the sub window (minimum)
-e Filter by the score of the best statistical window (minimum)
-f Filter by the coefficient of the variation (stnd dev BAIW oligos/ mean) for
the intensities in the BAIW, either treatment or control (singleton,
one chip driver) (maximum)
-g Remove particular intervals, enter a full path name for a tab delimited text
file containing rows with chromosome start stop.
-k Full path file name for the Interval
within will be processed. (Required)
Example: java -Xmx256M IntervalFilter -k /my/affy/res/ -e 50 -a 0.5
Depending on the size of the Interval
size of the java virtual machine using the -Xmx500M flag. Adjust accordingly in
response to out of memory errors and the available resources.
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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** Overlap Counter: March 2005 bdtnp.lbl.gov **
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OC performs a pairwise overlap comparison between each Interval array file within a
directory. Intervals are considered to overlap if they share 1bp in common. Sets of
overlapping and non-overlapping Intervals, for each file, can be written to disk. use
the -p option to compare interval peaks printing the closest.
Parameters:
-f Full path file name for a directory containing Interval files, required.
-n The number of Intervals to compare. Enter say 200 to compare the top 200 after
sorting. If they don't exist, all will be used. Default is all.
-s Sort Intervals by the median fold difference of the sub window,
default is to use the best mean intensity (ratio or difference) Window in
the Interval.
-t Sort Intervals by the best statistical scoring Window.
-m Max gap, default is 0bp. Negative values force an overlap.
-p Print distance to closest interval peak.
-w Write the overlapping and non-overlapping Interval files to disk, the default is no.
Example: java -Xmx128M OverlapCounter -f /affy/res/Intervals/ -n 250 -s -w -m -100
You may need to increase the heap size of the java virtual machine using the -Xmx
flag. Adjust accordingly in response to out of memory errors and the available
resources. Use a machine with >2GB of ram, otherwise it may run rather slowly.
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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** Map Regions to Intervals: June 2005 bdtnp.lbl.gov **
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MRTI performs a comparison between an array of Intervals and a text regions file
(Chromosome tab Start tab Stop tab Notes). Objects are considered to overlap if they
share 1bp in common. Intervals will be sorted by the median ratio of the best sub
window.
Parameters:
-f Full path file name for the Interval
-r Full path to the regions file, tab delimited 'chr start stop notes'. Be sure
the chromosome names for the regions are the same used by the intervals.
Example: java -Xmx128M MapRegionsToIntervals -f /affy/res/Intervals.res -r
/affy/posControls.txt
You may need to increase the heap size of the java virtual machine using the -Xmx
flag. Adjust accordingly in response to out of memory errors and the available
resources.
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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** Interval Plotter: May 2005 bdtnp.lbl.gov **
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IP plots and saves graphs for serialized Interval
data from the ScoreIntervals, FindSubBindingRegion, and LoadIntervalOligoInformation
programs prior to running the IntervalPlotter. What is plotted are graphs for the
averaged treatment intensity, the averaged control intensity, the average difference,
the average fold difference, a smoothed trimmed mean ratio, peak picks,the best window
by the ave intensity test, the best window by the stat test, the best sub window
by the average intensity test, centered PSPM hit scores, the number of 1bp mismatches
for each oligo in the genome, and the treatment and control intensities for each
individual processed cel file. Click and or drag to fetch the coordinates and sequence
for a selected region. Columns in console: interval rank, median ratio best sub window,
trimmed mean score for the closest oligo if just one click or the max trimmed mean
score within the dragged box, chromosome, start, stop, and sequence.
-f Full path file or directory name for the data loaded Interval
-t Sort Intervals by statistical score, default is to sort by Average Intensity
Difference score for the best Window within the Interval.
-w Sort Intervals by sub window median intensity fold difference.
-s Score cut off, plot everything above this score, defaults to all.
-r Rank cut off, plot everything above this rank, ie the top 200, defaults to all.
-q Rank cut off, plot everything below this rank, defaults to all.
-p Save plots to disk, default is no.
-m Magnify saved plots (2 twice as big, 3 three times as big...), default is none.
-a Anti alias saved plots, good for printed figures, bad for computer display,
default is no.
-b Hide the PSPM graphs.
Example: java IntervalPlotter -f /affy/res/Z.resAll -t -s 50 -r 200 -p -m 1.5 -a
Depending on the size of the Interval
size of the java virtual machine using the -Xmx500M flag. Adjust accordingly in
response to out of memory errors and the available resources.
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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** Interval Report Printer: June 2005 bdtnp.lbl.gov **
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IRP prints reports in spread sheet format or as detailed pages for Interval
Use the following options:
-f Full path file name for the Interval
within will be processed. (Required)
-t Sort Intervals by statistical score, default is to sort by the ratio score
-w Sort Intervals by the median ratio of the best sub window.
-s Score cut off, print everything above this score, defaults to all
-r Rank cut off, prints everything above this rank, ie the top 200, defaults to all
-p Print sequences, default is no
-a Print best intensity window sequence in summary line instead of interval sequence.
-b Print tab delimited summary line, default is to print a detailed report.
Example: java IntervalReportPrinter -f /my/affy/res/ -t -s 50 -r 200 -p -b
Depending on the size of the Interval
size of the java virtual machine using the -Xmx500M flag. Adjust accordingly in
response to out of memory errors and the available resources.
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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** Interval Graph Printer: Jan 2005 bdtnp.lbl.gov **
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IGP converts serialized Interval
Affymetrix' IGB. Files will be written to the data directory.
Use the following options when running IGP:
-f Full path file name for the Interval
within will be processed. (Required)
-t Sort Intervals by statistical score, default is to sort by the ratio score of the
best Intensity Window within the Interval.
-w Sort Intervals by the median fold difference of the best sub window.
-s Score cut off, print everything above this score, defaults to all
-r Rank cut off, prints everything above this rank, ie the top 200, defaults to all
-g Print goal post Interval representations, default is to print oligo scores
-d Print mean relative difference scores, default is to print mean oligo ratio scores
-c Chromosome prefix to prepend onto each .sgr line. (This is sometimes needed to match
IGB's quickload seqIDs.)
Example: java IntervalGraphPrinter -f /my/affy/res/ -s 50 -r 200
Depending on the size of the Interval
size of the java virtual machine using the -Xmx500M flag. Adjust accordingly in
response to out of memory errors and the available resources.
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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** Interval GFF Printer: June 2005 bdtnp.lbl.gov **
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IGP prints a GFF3 txt file given a serialized Interval file sorted by the median ratio
of the best sub window. Use the following options:
-f Full path file name for the Interval
within will be processed and saved to the same GFF3 file.
Example: java IntervalGFFPrinter -f /my/affy/res/
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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** Binding Region Graph Printer: March 2005 bdtnp.lbl.gov **
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BRGP converts a Binding Region Picks txt file (from the IntensityPlotter: rank
subWinMedianScore trimmedMeanPickScore chrom start stop seq) to an .sgr file for
import into Affymetrix's IGB.
Use the following options when running BRGP:
-f Full path file name for the .txt picks file, if a directory is specified, all '.txt'
files found within will be processed. (Required)
Example: java BindingRegionGraphPrinter -f /my/affy/res/hbPicks.txt
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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** Oligo Intensity Printer: June 2005 bdtnp.lbl.gov **
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OIP prints to file the treatment, control, and ratio intensity scores in a
.sgr text format for direct import into Affy's IGB.
Use the following options when running OIP:
-b Full path directory name for the 'BPMapFiles' generated by the BPMapProcessor
(required).
-t The full path file name for the serialized float
-c The full path file name for the serialized float
Example: java -Xmx256M OligoIntensityPrinter -b /affy/BPMapFiles/ -t
/affy/t.celp -c /affy/c.celp
You will need to increase the heap size of the java virtual machine using the -Xmx
flag. Adjust accordingly in response to out of memory errors and the available
resources. Use a machine with >2GB of ram, otherwise it will run rather slowly.
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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** Intensity Printer: June 2005 bdtnp.lbl.gov **
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IP prints to file intensity scores in a .sgr text format for direct import into
Affy's IGB.
Use the following options when running IP:
-b Full path directory name for the 'BPMapFiles' generated by the BPMapProcessor
(required).
-i The full path file name for the serialized float
Example: java -Xmx256M IntensityPrinter -b /affy/BPMapFiles/ -i
/affy/t.celp
You will need to increase the heap size of the java virtual machine using the -Xmx
flag. Adjust accordingly in response to out of memory errors and the available
resources. Use a machine with >2GB of ram, otherwise it will run rather slowly.
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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** Annotate Regions: Jan 2005 bdtnp.lbl.gov **
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Annotates a picks file finding surrounding protein coding genes.
-g Full path file name for the DmelRel4.0 GFF3 file.
-p Full path file name for the binding region picks or Interval file.
-c Full path file name for the Filtered CG names file (optional)
-b Size of neighborhood in bp, default is 10000 (optional)
-r Number of random trials (optional)
-n Just print number of neighbors for random trials (optional)
-s Skip filtering GFF file
Example: java -Xmx128M AnnotateRegions -g /dmel/dmel_RELEASE4.0.gff3 -p
/affy/zeste/finalPicks.txt -c /dmel/CGs.txt
You may need to increase the heap size of the java virtual machine using the -Xmx500M
flag in response to out of memory errors and the available resources.
Questions, comments, suggestions? Contact danix@lbl.gov or superfly@lbl.gov.
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