Mutation effect on sites advanced (analysis)

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Analysis title
GTRD-Mutation-effect-on-sites-advanced-icon.png Mutation effect on sites advanced
Provider
Institute of Systems Biology
Class
MutationAffectOnSitesAdvanced
Plugin
biouml.plugins.gtrd (GTRD)

Parameters:

  • Input VCF track – Input track in VCF format
  • Genome – Reference genome
    • 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
  • Profile – Predefined set of site models
  • Score type – The type of position weight matrix score
  • Score difference – Minimal site score difference between reference and alternative sequences
  • Independent variations – Treat each variation independently
  • Target gene TSS upstream – When searching for target genes, match TF binding sites to this distance upstream of TSS.
  • Target gene TSS downstream – When searching for target genes, match TF binding sites to this distance downstream of TSS.
  • One nearest target gene – Report only one target gene nearest to TSS.
  • TF class depth – TF class depth
  • Add transpath annotation – Transpath pathways annotation will be added to the output table
  • Transpath – Transpath
  • Add HumanPSD annotation – HumanPSD disease annotation will be added to the output table
  • HumanPSD – HumanPSD
  • Output table – Output table
  • Site gain track – Resulting track with site gain events
  • Site loss track – Resulting track with site gain events
  • Important mutations – Track of mutations that affects binding sites
  • Summary table – Summary table giving site model frequencies per mutation
  • Selected GTRD peaks/metaclusters – Selected GTRD peaks/metaclusters
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