User talk:RobertBuels

(add on JBrowse)

JBrowse Configuration Guide

• Configuration Guide
  • Formatting reference sequences (e.g. from FASTA files, or a Chado database)
  • Creating feature tracks (e.g. from BED or GFF files, a Chado database, or the UCSC genome browser)
  • Creating image tracks (e.g. from WIG files)
  • Making features searchable by name
  • Removing tracks
  • Compressing data stored on the server
  • Using callbacks to customize feature tracks

• Additional topics:
  • Using Configuration Files with biodb-to-json.pl
  • Using a Database

Anonymous Usage Statistics

JBrowse instances report usage statistics to the JBrowse developers. This data is very important to the JBrowse project, since it is used to make the case to grant agencies for continuing to fund JBrowse development. No research data is transmitted, the data collected is limited to standard Google Analytics, along with a count of how many tracks the JBrowse instance has, how many reference sequences are present, their average length, and what types of tracks (wiggle, feature, etc) are present. Users can disable usage statistics by setting suppressUsageStatistics: true in the JBrowse configuration.

Searchable Names

generate-names.pl

This script makes it possible to search for features by label (the visible name below a feature in JBrowse) and/or by alias (a secondary name that is not visible in the web browser, but may be present in the JSON used by the JBrowse client). For tracks that are added using flatfile-to-json.pl or biodb-to-json.pl, searchability depends on how the 'autocomplete' option is used. If a track is input with the autocomplete option set to 'alias', for instance, features will be searchable by alias after generate-names.pl is run (provided that alias names are present in the original data source). For tracks added using ucsc-to-json.pl, features will be searchable by label after running generate-names.pl.

To search for a term, use the text box at the top of the JBrowse window.

Basic syntax:

bin/generate-names.pl [options]

Note that generate-names.pl does not require any arguments. However, some options are available:

Option	Value
dir	A path to the output directory (default is 'data/names' in the current directory).
thresh	A lower-bound on the Patricia trie chunk size. Specifically, the lowest possible chunk size is (thresh + 1). The default value is 200. In this context, a chunk is a group of connected Patricia trie nodes that can be visualized as a single entity, and the chunk size is the total number of genomic features contained in a chunk. The lower the value of thresh, the more chunks there will be.
verbose	This setting causes information about the division of nodes into chunks to be printed to the screen.