Difference between revisions of "Compare TFBS mutations (analysis)"
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;Analysis title | ;Analysis title | ||
| − | :[[File: | + | :[[File:Mutations-Compare-TFBS-mutations-icon.png]] Compare TFBS mutations |
;Provider | ;Provider | ||
:[[Institute of Systems Biology]] | :[[Institute of Systems Biology]] | ||
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==== Description ==== | ==== Description ==== | ||
| − | Find transcription factors that have different proportions of site losses(gains) in two datasets | + | Find transcription factors that have different proportions of site losses(gains) in two datasets. |
==== Parameters: ==== | ==== Parameters: ==== | ||
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* '''Profile''' – Predefined set of site models | * '''Profile''' – Predefined set of site models | ||
* '''P-value cutoff''' – P-value cutoff | * '''P-value cutoff''' – P-value cutoff | ||
| + | * '''Input size limit''' – If the input VCF larger than this limit, the VCF track will be randomly subsampled to this size. | ||
* '''Site gains table''' – Table with transcription factors which change frequency of site gains between experiment and control | * '''Site gains table''' – Table with transcription factors which change frequency of site gains between experiment and control | ||
* '''Site losses table''' – Table with transcription factors which change frequency of site losses between experiment and control | * '''Site losses table''' – Table with transcription factors which change frequency of site losses between experiment and control | ||
[[Category:Analyses]] | [[Category:Analyses]] | ||
| − | [[Category: | + | [[Category:Mutations (analyses group)]] |
[[Category:ISB analyses]] | [[Category:ISB analyses]] | ||
[[Category:Autogenerated pages]] | [[Category:Autogenerated pages]] | ||
Latest revision as of 18:15, 9 December 2020
- Analysis title
Compare TFBS mutations
- Provider
- Institute of Systems Biology
- Class
CompareTFBSMutations- Plugin
- ru.biosoft.bsa (Bio-sequences analyses plugin)
[edit] Description
Find transcription factors that have different proportions of site losses(gains) in two datasets.
[edit] Parameters:
- Experiment VCF track – Experiment VCF track
- Control VCF track – Control VCF track
- 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
- P-value cutoff – P-value cutoff
- Input size limit – If the input VCF larger than this limit, the VCF track will be randomly subsampled to this size.
- Site gains table – Table with transcription factors which change frequency of site gains between experiment and control
- Site losses table – Table with transcription factors which change frequency of site losses between experiment and control
