GTEX Mutation effect on sites (analysis)
From BioUML platform
- Analysis title
- GTEX Mutation effect on sites
- Institute of Systems Biology
- biouml.plugins.gtex (GTEX)
- 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.
- 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