Difference between revisions of "SNP matching (analysis)"

From BioUML platform
Jump to: navigation, search
(Plugin name added)
(Automatic synchronization with BioUML)
 
(5 intermediate revisions by one user not shown)
Line 1: Line 1:
 
;Analysis title
 
;Analysis title
:[[File:BSA-SNP-matching-icon.png]] SNP matching
+
:[[File:Mutations-SNP-matching-icon.png]] SNP matching
 
;Provider
 
;Provider
 
:[[Institute of Systems Biology]]
 
:[[Institute of Systems Biology]]
 +
;Class
 +
:{{Class|biouml.plugins.ensembl.analysis.SNPListToTrack}}
 
;Plugin
 
;Plugin
:ru.biosoft.bsa (Bio-sequences analyses plugin)
+
:[[Biouml.plugins.ensembl (plugin)|biouml.plugins.ensembl (Support for Ensembl database and Ensembl-specific analyses)]]
  
 
==== Description ====
 
==== Description ====
Converts given list of SNPs to track and matches them to the genes. User should supply table where row identifiers are SNP names like <nowiki>'</nowiki>rs11111111<nowiki>'</nowiki>
+
Converts given list of SNPs to track and matches them to the genes. User should supply table where row identifiers are SNP names like <nowiki>'</nowiki>rs11111111<nowiki>'</nowiki>.
  
 
==== Parameters: ====
 
==== Parameters: ====
  
 
* '''Table''' – Table of source genes
 
* '''Table''' – Table of source genes
* '''Species''' – Taxonomical species
+
* '''Ensembl''' – Ensembl database version
 
* '''5<nowiki>'</nowiki> region size''' – Include 5<nowiki>'</nowiki> region (promoter) of given size in bp
 
* '''5<nowiki>'</nowiki> region size''' – Include 5<nowiki>'</nowiki> region (promoter) of given size in bp
 
* '''3<nowiki>'</nowiki> region size''' – Include 3<nowiki>'</nowiki> region of given size in bp
 
* '''3<nowiki>'</nowiki> region size''' – Include 3<nowiki>'</nowiki> region of given size in bp
 
* '''Output non-matched''' – Whether to include in output table and track SNP<nowiki>'</nowiki>s which were not matched to any gene
 
* '''Output non-matched''' – Whether to include in output table and track SNP<nowiki>'</nowiki>s which were not matched to any gene
 
* '''Column to copy''' – Name of additional column to be copied to created genes table
 
* '''Column to copy''' – Name of additional column to be copied to created genes table
 +
* '''Ignore empty values''' – Ignore empty values during aggregator work
 
* '''Aggregator''' – Operation to perform on column values if several SNP<nowiki>'</nowiki>s matched to single gene (<nowiki>'</nowiki>minimum<nowiki>'</nowiki>,<nowiki>'</nowiki>maximum<nowiki>'</nowiki>,<nowiki>'</nowiki>sum<nowiki>'</nowiki>,<nowiki>'</nowiki>average<nowiki>'</nowiki>)
 
* '''Aggregator''' – Operation to perform on column values if several SNP<nowiki>'</nowiki>s matched to single gene (<nowiki>'</nowiki>minimum<nowiki>'</nowiki>,<nowiki>'</nowiki>maximum<nowiki>'</nowiki>,<nowiki>'</nowiki>sum<nowiki>'</nowiki>,<nowiki>'</nowiki>average<nowiki>'</nowiki>)
 
* '''Output track''' – Path to output track
 
* '''Output track''' – Path to output track
Line 23: Line 26:
  
 
[[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-SNP-matching-icon.png SNP matching
Provider
Institute of Systems Biology
Class
SNPListToTrack
Plugin
biouml.plugins.ensembl (Support for Ensembl database and Ensembl-specific analyses)

[edit] Description

Converts given list of SNPs to track and matches them to the genes. User should supply table where row identifiers are SNP names like 'rs11111111'.

[edit] Parameters:

  • Table – Table of source genes
  • Ensembl – Ensembl database version
  • 5' region size – Include 5' region (promoter) of given size in bp
  • 3' region size – Include 3' region of given size in bp
  • Output non-matched – Whether to include in output table and track SNP's which were not matched to any gene
  • Column to copy – Name of additional column to be copied to created genes table
  • Ignore empty values – Ignore empty values during aggregator work
  • Aggregator – Operation to perform on column values if several SNP's matched to single gene ('minimum','maximum','sum','average')
  • Output track – Path to output track
  • Output SNP table – Path to output table with additional annotation
  • Output genes table – Path to output table containing all the genes matched to SNPs
Personal tools
Namespaces

Variants
Actions
BioUML platform
Community
Modelling
Analysis & Workflows
Collaborative research
Development
Virtual biology
Wiki
Toolbox