Bio::Graphics::Browser2::DataLoader::useq - data loader for the USeq archive
A data loader for the USeq archive, recognized by the file extension
<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.
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
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.