Difference between revisions of "SNP matching (analysis)"

Revision as of 16:32, 12 March 2019

Analysis title: SNP matching
Provider: Institute of Systems Biology
Class: SNPListToTrack
Plugin: biouml.plugins.ensembl (Support for Ensembl database and Ensembl-specific analyses)

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'

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
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

@@ Line 4: / Line 4: @@
 :[[Institute of Systems Biology]]
 ;Class
-:{{Class|ru.biosoft.bsa.snp.SNPListToTrack}}
+:{{Class|biouml.plugins.ensembl.analysis.SNPListToTrack}}
 ;Plugin
-:[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]]
+:[[Biouml.plugins.ensembl (plugin)|biouml.plugins.ensembl (Support for Ensembl database and Ensembl-specific analyses)]]
 ==== Description ====
@@ Line 14: / Line 14: @@
 * '''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
 * '''3<nowiki>'</nowiki> region size''' – Include 3<nowiki>'</nowiki> region of given size in bp