Bio::Graphics::Browser2::DataLoader::useq3pm

Overview

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.