NAME

       Bio::Graphics::Browser2::DataLoader::useq - data loader for the USeq archive

DESCRIPTION

       A data loader for the USeq archive, recognized by the file extension ".useq".  See
       <http://useq.sourceforge.net/useqArchiveFormat.html> for information regarding the file
       format. Briefly, this format can store either genomic intervals with or without text
       and/or scores, or quantitative scores along a chromosome (point data).

       There is currently no native BioPerl adaptor for the USeq archive. Upon upload, the file
       is converted to either a UCSC BigBed or BigWig format, depending upon the file contents.
       Stranded point data may be converted into two BigWig files, each for the Plus and Minus
       strand. Configuration files are generated as appropriate for the converted files.

SETUP

       To process the USeq archive, the USeq package (<http://useq.sourceforge.net> must be
       installed in a globally accessible path. This location is searched upon initiation. Common
       paths to search include "/usr", "/usr/local", "/opt", "/opt/gbrowse", "/data",
       "/data/opt", and "/Applications", in that order.

       The USeq App "USeq2UCSCBig" (a jar file) is used to convert the USeq archive. This app
       requires three binary executables: "java" and the two UCSC utilities "bedToBigBed" and
       "wigToBigWig". These are searched for in the environment $PATH variable.  The UCSC
       utilities are available at <http://hgdownload.cse.ucsc.edu/admin/exe/>.  The USeq Apps
       requires Java 1.6+.

       Failure to find the paths for all three will result in failure to process the .useq file.

AUTHOR

        Timothy J. Parnell, PhD
        Dept of Oncological Sciences
        Huntsman Cancer Institute
        University of Utah
        Salt Lake City, UT, 84112

       This package is free software; you can redistribute it and/or modify it under the terms of
       the GPL (either version 1, or at your option, any later version) or the Artistic License
       2.0.

perl v5.38.2                                2024-03Bio::Graphics::Browser2::DataLoader::useq(3pm)