Ribo-Seq and mRNA features forming (analysis)

Analysis title

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