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  • PeakAnalyzer - Downloads

    PeakSplitter 1.0 (tar/gz)

    Release notes:

    ////////////////////////////////////////////////////////////////////////////////
    INSTALLATION
    ////////////////////////////////////////////////////////////////////////////////
    
    Please check the following instructions to complete your installation.
    
    * Install from source
    PeakSplitter uses external libraries
    1. The iMatix SFL, Copyright  1991-2000 iMatix Corporation 
    2. zlib - Copyright (C) 1995-2005 Jean-loup Gailly and Mark Adler
    3.tclap - Copyright  2003,2004,2005,2006,2009 Michael E. Smoot
    
    zlib and SFL libraries have to be compiled before installing PeakSplitter.
    
    1. Open up a command terminal, go to the directory "PeakSplitter_v1" where you have uncompressed PeakSplitter.
    
    2. Within this directory, go to "SFL/Release" directory and run the makefile using 
    make (or make -f makefile)
    
    3. Return to the directory "PeakSplitter_v1", then go to the "Zlib/Release" directory and run the makefile
    make (or make -f makefile)
    
    4. Now you are ready to install PeakSplitter. Return to the directory "PeakSplitter_v1", and run the makefile
    make (or make -f makefile)
    An executable file named "PeakSplitter" will be generated in this folder.
    
    To run the program type ./PeakSplitter, and ./PeakSplitter --help in order to get some help on the input parameters.
    
    You can move the "PeakSplitter" exe file to anywhere on your file system and set the PATH to this folder.
    
    
    ////////////////////////////////////////////////////////////////////////////////
    USAGE
    ////////////////////////////////////////////////////////////////////////////////
    
    Usage: PeakSplitter <-p peakfile> <-w wig file/folder> <-o output folder> [options]
    
    Options:
    
       --version
         Displays version information and exits.
    
       -h,  --help
         Displays usage information and exits.
    
       -p ,  --peakFile 
         (required)  input peak file
    
       -w ,  --wigFile 
         (required)  input wig file or folder
    
       -o ,  --outDir 
         (required)  output folder
    
       -c ,  --cutoff 
         height cutoff (default 5)
    
       -v ,  --valley 
         float value to determine the valley depth required for peak separation
         (default 0.6)
    
        -f,  --fetch
         whether to fetch subpeaks sequences or not (default true)
    
        -u ,  --url 
         Das url where to get sequences from (default is for human
         "http://www.ensembl.org/das/Homo_sapiens.GRCh37.reference")
        
        -n ,  --numSeq 
         number of best peak sequences to fetch (default 300)
    
        -l ,  --length 
         length of sequence to fetch (default 60)
    
    
    *** -p/ --peakFile 
    This is a REQUIRED parameter for PeakSplitter. 
    The file lists the genomic coordinates output by a peak calling program 
    (or obtained in some other way). The format should be tab/space delimited, 
    where each locus is described by its "chromosome", "start" and "end" location.
    This file should be sorted by chromosome and start position.
    PLEASE REMOVE ANY HEADER LINES FROM THE FILE IF THESE ARE PRESENT
    
    *** -w/--wigFile
    This is a REQUIRED parameter for PeakSplitter.
    This can be a wig file OR a wig folder that contains one wig file for each chromosome, 
    where the wig file describes the signals (usually number of reads) along the genome and
    are created by the peak-calling program that generated the peak file. 
    PeakSplitter supports wig files in VariableStep or Bedgraph formats. 
    The wig header lines, "track type" and "variableStep" (when using VariableStep format)
    are required. 
    The files can be zipped or gzipped, so it's not necessary to uncompress them.
    
    wig file names for each chromosme (under wig folder) should contain the word "chr" + 
    chromosome number, for example "my.chr12.wig".
    
    *** -o/--outDir
    This is a REQUIRED parameter for PeakSplitter.
    An output directory must be specified where PeakSplitter can write the result files. 
    
    *** -x/--prefix
    string to add to output file names, for example when the same peak files are analyzed 
    using different parameters.
    
    *** -c/--cutoff
    Height cutoff (default 5). Only subpeaks with at least this number of reads in 
    their summit region will be reported.
    
    *** -v/--valley 
    Real value indicating the valley depth required for peak separation (default 0.6). 
    Local maxima regions are found within each peak and the height of neighboring local 
    maxima are compared. The lowest value is multiplied by the valley real-valued number 
    to yield the minimum depth required to separate the two peaks. 
    For example, a value of 0.5 means that the height of the valley should be less than 
    half the height of its summits in order for them to be separated.
    
    *** -f/--fetch
    By default, PeakSplitter will fetch the subpeak sequences near their summit region. 
    In order to turn this feature off set it to be
    -f false
    
    *** -u/--url
    The sequences are exported directly from the DAS Ensembl database.
    The user has to specify the DAS URL for the organism of interest.
    The DAS URL for the human database is "http://www.ensembl.org/das/Homo_sapiens.GRCh37.reference", 
    and URLs for other organisms can be found at: "http://www.ensembl.org/das/dsn"
    
    *** -n/--numSeq
    Number of best subpeak sequences to fetch (those with the highest numbers of reads 
    in their summit region). These sequences can be used as input for motif prediction 
    tools such as MEME. 
    The default number is 300. This is the maximum number of sequences the web-based 
    version of MEME will accept (more sequences can be input when run locally).
    
    *** -l/--length
    Length of sequence to fetch (default 60)
    The sequences are retrieved near the summit region. 
    If the length is 60, 30 bp will be included upstream to the peak summit position, 
    and 30 downstream. The total sequence length will be 61.
    
    ////////////////////////////////////////////////////////////////////////////////
    OUTPUT FILES
    ////////////////////////////////////////////////////////////////////////////////
    
    If the -x parameter is specified, all output file names will start with the 
    base string following the -x flag.
    
    1. peakFileName.subpeaks.inputFileNameSuffix
    For example, if the input peak file is "myPeaks.test", 
    the output file will be "myPeaks.subpeaks.test"
    
    This is a tab-delimited file which contains information about subpeaks, including:
    a. Chromosome name
    b. Start position of the subpeak
    c. End position of the subpeak 
    d. Number of reads in the peak summit position 
    e. Subpeak summit position relative to the start position of the subpeak region.
    
    2. peakFileName(without suffix).bestSubpeaks.fa
    For example, if the input peak file is "myPeaks.test", the output file will be 
    "myPeaks.bestSubpeaks.fa
    
    This is a fasta file, containing the sequences of the best subpeaks 
    (those with highest numbers of reads in their summit position).
    


    Changelog:

    PeakSplitter 1.0 (tar/gz)

    Release notes:

    ////////////////////////////////////////////////////////////////////////////////
    INSTALLATION
    ////////////////////////////////////////////////////////////////////////////////
    
    This folder contains the executable jar file PeakSplitter.jar and the archive
    PeakSplitter.src.zip, which contains source directories and the ant build file.
    You can move the "PeakSplitter.jar" exe file to anywhere in your file system and 
    set the PATH to this location.
    
    ////////////////////////////////////////////////////////////////////////////////
    USAGE
    ////////////////////////////////////////////////////////////////////////////////
    
    You should have Java 1.5 or later installed.
    In order to launch the program, open a terminal window, go to the folder
    where the jar file is located, and type
    
    java -jar PeakSplitter.jar <-p peakfile> <-w wig file/folder> <-o output folder> [options]
    
    Options include:
    
    -help,-?                        displays help information
    -p,--peakFile           input peak file
    -w,--wigFile            input wig file or folder
    -o,--outDir             output folder
    -x,--prefix             string to add to output file names
    -c,--cutoff    height cutoff (default 5)
    -v,--valley              float value to determine the valley depth required for peak separation (default 0.6)
    -f,--fetch             whether to fetch subpeaks sequences or not (default true)
    -u,--url                Das url (default is for human "http://www.ensembl.org/das/Homo_sapiens.GRCh37.reference"
    -n,--numSeq    number of best peak sequences to fetch (default 300)
    -l,--length    length of sequence to fetch (default 60)
    
    
    *** -p/ --peakFile 
    This is a REQUIRED parameter for PeakSplitter. 
    The file lists the genomic coordinates output by a peak calling program 
    (or obtained in some other way). The format should be tab/space delimited, 
    where each locus is described by its "chromosome", "start" and "end" location.
    This file should be sorted by chromosome and start position.
    PLEASE REMOVE ANY HEADER LINES FROM THE FILE IF THESE ARE PRESENT
    
    *** -w/--wigFile
    This is a REQUIRED parameter for PeakSplitter.
    This can be a wig file OR a wig folder that contains one wig file for each chromosome, 
    where the wig file describes the signals (usually number of reads) along the genome and
    are created by the peak-calling program that generated the peak file. 
    PeakSplitter supports wig files in VariableStep or Bedgraph formats. 
    The wig header lines, "track type" and "variableStep" (when using VariableStep format)
    are required. 
    The files can be zipped or gzipped, so it's not necessary to uncompress them.
    
    wig file names for each chromosme (under wig folder) should contain the word "chr" + 
    chromosome number, for example "my.chr12.wig".
    
    *** -o/--outDir
    This is a REQUIRED parameter for PeakSplitter.
    An output directory must be specified where PeakSplitter can write the result files. 
    
    *** -x/--prefix
    string to add to output file names, for example when the same peak files are to be 
    analyzed using different parameters.
    
    *** -c/--cutoff
    Height cutoff (default 5). Only subpeaks with at least this number of reads in 
    their summit region will be reported.
    
    *** -v/--valley 
    Real value indicating the valley depth required for peak separation (default 0.6). 
    Local maxima regions are found within each peak and the height of neighboring local 
    maxima are compared. The lowest value is multiplied by the valley real-valued number 
    to yield the minimum depth required to separate the two peaks. 
    For example, a value of 0.5 means that the height of the valley should be less than 
    half the height of its summits in order for them to be separated.
    
    *** -f/--fetch
    By default, PeakSplitter will fetch the subpeak sequences near their summit region. 
    In order to turn this feature off set it to be
    -f false
    
    *** -u/--url
    The sequences are exported directly from the DAS Ensembl database.
    The user has to specify the DAS URL for the organism of interest.
    The DAS URL for the human database is "http://www.ensembl.org/das/Homo_sapiens.GRCh37.reference", 
    and URLs for other organisms can be found at: "http://www.ensembl.org/das/dsn"
    
    *** -n/--numSeq
    Number of best subpeak sequences to fetch (those with the highest numbers of reads 
    in their summit region). These sequences can be used as input for motif prediction 
    tools such as MEME. 
    The default number is 300. This is the maximum number of sequences the web-based 
    version of MEME will accept (more sequences can be input when run locally).
    
    *** -l/--length
    Length of sequence to fetch (default 60)
    The sequences are retrieved near the summit region. 
    If the length is 60, 30 bp will be included upstream to the peak summit position, 
    and 30 downstream. The total sequence length will be 61.
    
    ////////////////////////////////////////////////////////////////////////////////
    OUTPUT FILES
    ////////////////////////////////////////////////////////////////////////////////
    
    If the -x parameter is specified, all output file names will start with the 
    base string following the -x flag.
    
    1. peakFileName.subpeaks.inputFileNameSuffix
    For example, if the input peak file is "myPeaks.test", 
    the output file will be "myPeaks.subpeaks.test"
    
    This is a tab-delimited file which contains information about subpeaks, including:
    a. Chromosome name
    b. Start position of the subpeak
    c. End position of the subpeak 
    d. Number of reads in the peak summit position 
    e. Subpeak summit position relative to the start position of the subpeak region.
    
    2. peakFileName(without suffix).bestSubpeaks.fa
    For example, if the input peak file is "myPeaks.test", the output file will be 
    "myPeaks.bestSubpeaks.fa
    
    This is a fasta file, containing the sequences of the best subpeaks 
    (those with highest numbers of reads in their summit position).
    


    Changelog:

     

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