Lincoln D. Stein > GBrowse-2.55 > Bio::Graphics::Browser2::DataLoader::useq

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NAME ^

Bio::Graphics::Browser2::DataLoader::useq

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.

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