FiRePat processing parameters

FiRePat processing parameters

The user can specify the following processing parameters. All these parameters have preset default values which are used if the user does not change them.

  • Whether sRNA data should be filtered, the┬ádefault is yes.
  • The percentage of sRNA sequences for which data should be retained when filtering, the default is10%.
  • Whether non-sRNA data should be filtered, the default is yes.
  • The minimum expression level for non-sRNA data to be retained, the default is 10.
  • Which correlation method should be used: Kendall, Pearson or Spearman. The default method is Pearson.
  • Whether local correlations should be used, the default is no.
  • The minimum window width to use for local correlations. The lowest and default value is 4. If less than 4 is entered, the value will be reset to 4.
  • Absolute correlation threshold value. The value below which a pair of sequences will not be retained. The default is 0.9, i.e. sequence pairs will only be retained if their correlation is 0.9 or greater, or -0.9 or less.

A suite of tools for analysing micro RNA and other small RNA data from High-Throughput Sequencing devices