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

        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 v5.40.0                                       2024-10-20              Bio::Graphics:...ataLoader::useq(3pm)

       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.

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

       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.