Difference between revisions of "Compare TFBS mutations (analysis)"

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;Analysis title
 
;Analysis title
:[[File:BSA-Compare-TFBS-mutations-icon.png]] Compare TFBS mutations
+
:[[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:BSA (analyses group)]]
+
[[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
Mutations-Compare-TFBS-mutations-icon.png 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
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