HPeak: A HMM-based algorithm for defining read-enriched regions from massive parallel sequencing data

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Please check the following instructions to complete your installation.

Set up


The software suite was written by Perl and C++. Users may require to download a copy of Perl disctribution and compile the C++ source code to complete the installation. Windows users may download a Perl distribution from ActivatePerl.

For installation, please extract the downloaded source package using any archive program. The full software package includes a script folder and a supplementary data folder. The first contains all perl scripts and C++ source code. The latter folder includes the necessary information files for extracting genomic sequences and average phastCons scores for individual bases. Users may directly download unmasked sequences from UCSC (http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/chromFa.zip) and extract them to data folder. Please see the example directory structure below. For phastCons scores, we pre-compiled the Conservation scores for alignments of 16 vertebrate genomes with Human provided by UCSC genome website (http://hgdownload.cse.ucsc.edu/goldenPath/hg18/phastCons17way/).

One should set path to the /scripts/ directory or add the full path to each command. E.g., perl ~/scripts/summary.pl. The proper directory structure is as follows:

<DIR>    scripts
<DIR>    scirpts\data
FILE       scripts\data\refFlat.out
<DIR>    scripts\data\chromFa\
<DIR>    scripts\data\phastCons\

 

 


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