SNP matching (analysis)

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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)

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'.

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
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