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.IX Title "Bio::Graphics::Browser2::DataLoader::useq 3pm"
.TH Bio::Graphics::Browser2::DataLoader::useq 3pm "2018-10-03" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Graphics::Browser2::DataLoader::useq \- data loader for the USeq archive
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
A data loader for the USeq archive, recognized by the file extension \*(L".useq\*(R". 
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).
.PP
There is currently no native BioPerl adaptor for the USeq archive. Upon upload, the 
file is converted to either a \s-1UCSC\s0 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.
.SH "SETUP"
.IX Header "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 \*(L"/usr\*(R", \*(L"/usr/local\*(R", \*(L"/opt\*(R", 
\&\*(L"/opt/gbrowse\*(R", \*(L"/data\*(R", \*(L"/data/opt\*(R", and \*(L"/Applications\*(R", in that order.
.PP
The USeq App \*(L"USeq2UCSCBig\*(R" (a jar file) is used to convert the USeq archive. This 
app requires three binary executables: \*(L"java\*(R" and the two \s-1UCSC\s0 utilities \*(L"bedToBigBed\*(R" 
and \*(L"wigToBigWig\*(R". These are searched for in the environment \f(CW$PATH\fR variable. 
The \s-1UCSC\s0 utilities are available at <http://hgdownload.cse.ucsc.edu/admin/exe/>. 
The USeq Apps requires Java 1.6+.
.PP
Failure to find the paths for all three will result in failure to process the .useq 
file.
.SH "AUTHOR"
.IX Header "AUTHOR"
.Vb 5
\& Timothy J. Parnell, PhD
\& Dept of Oncological Sciences
\& Huntsman Cancer Institute
\& University of Utah
\& Salt Lake City, UT, 84112
.Ve
.PP
This package is free software; you can redistribute it and/or modify
it under the terms of the \s-1GPL\s0 (either version 1, or at your option,
any later version) or the Artistic License 2.0.