Ribo-Seq and mRNA features forming (analysis)

From BioUML platform
Revision as of 19:00, 13 February 2017 by BioUML wiki Bot (Talk | contribs)

(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search
Analysis title
Default-analysis-icon.png Ribo-Seq and mRNA features forming
Provider
Institute of Systems Biology
Class
RiboSeqAndMrnaFeaturesForming
Plugin
biouml.plugins.bindingregions (Binding-regions related analyses)

Description

Create data matrix with Ribo-Seq and mRNA features and write it as TableDataCollection

Parameters:

  • Data set name – Select data set
  • Sequences collection – Select a source of nucleotide sequences
    • 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
  • Two tables for calculation of translation (initiation) efficiency, TE (TIE) – Two tables for calculation of translation (initiation) efficiency, TE (TIE)
    • Path to table with mRNA-Seq data – Path to table with mRNA-Seq data
    • Column name with mRNA-Seq reads number – Select column name with mRNA-Seq reads number
    • mRNA-Seq reads threshold – Transcripts for which mRNA-Seq reads number are grater than this threshold will be considered only
    • Path to table with Ribo-Seq data – Path to table with Ribo-Seq data
    • Column name with Ribo-Seq reads number – Select column name with Ribo-Seq reads number
    • Ribo-Seq reads threshold – Transcripts for which Ribo-Seq reads number are grater than this threshold will be considered only
    • Column name with start codon positions – Select column name with start codon positions
    • Column name with transcript names – Column name with transcript names
  • Path to folder with special data sets – Path to folder with special data sets
  • Start codon type – Start codon type
  • Order of start codon – Order of start codon
  • mRNA and Ribo-Seq features – Select mRNA and Ribo-Seq features
  • Sequence sample – Sequence sample
    • Are mRNA fragments near start codons? – Are mRNA fragments near start codons (or near stop codons)?
    • Left boundary of each mRNA fragment – Left boundary of each mRNA fragment with respect to start (or stop) codon
    • Right boundary of each mRNA fragment – Right boundary of each mRNA fragment with respect to start (or stop) codon
  • Paths to matrices – Paths to matrices
  • Do exclude missing data? – Do exclude missing data? (If 'no' then possible missing data will be included as NaN-values
  • Output table path – Path to the output table
Personal tools
Namespaces

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