Mutation effect on sites advanced (analysis)

Analysis title

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