Difference between revisions of "Mutation effect on sites advanced (analysis)"
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Revision as of 18:14, 9 December 2020
- 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