Difference between revisions of "Track coverage (analysis)"

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* '''Sequences''' – Collection of sequences
 
* '''Sequences''' – Collection of sequences
 
** '''Sequences source''' – Select database to get sequences from or <nowiki>'</nowiki>Custom<nowiki>'</nowiki> to specify sequences location manually
 
** '''Sequences source''' – Select database to get sequences from or <nowiki>'</nowiki>Custom<nowiki>'</nowiki> to specify sequences location manually
** '''Sequence collection''' – Sequence collection
+
** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> sequences source is selected
** '''Genome ID string''' – Something like <nowiki>'</nowiki>hg18<nowiki>'</nowiki> or <nowiki>'</nowiki>mm6<nowiki>'</nowiki>
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* '''Window size''' – Size of the window to average the coverage
 
* '''Window size''' – Size of the window to average the coverage
 
* '''Step''' – Number of bp to step (at least 1000)
 
* '''Step''' – Number of bp to step (at least 1000)

Revision as of 17:16, 6 June 2013

Analysis title
File:BSA-Track-coverage-icon.png Track coverage
Provider
Institute of Systems Biology
Class
TrackCoverageAnalysis
Plugin
ru.biosoft.bsa (Bio-sequences analyses plugin)

Description

Calculates the coverage of given track

Parameters:

  • Input track – Track to calculate coverage for
  • Sequences – Collection of sequences
    • Sequences source – Select database to get sequences from or 'Custom' to specify sequences location manually
    • Sequence collection – Specify path to folder containing sequences if 'Custom' sequences source is selected
  • Window size – Size of the window to average the coverage
  • Step – Number of bp to step (at least 1000)
  • Output empty intervals – When checked, intervals without single site will appear in the output table as well
  • Output table – Path to the output table
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