FiRePat output parameters

FiRePat output parameters

The user can specify the following processing parameters. All parameters have preset default values which are used if the user does not change them. N.B. any existing files will be overwritten without warning.

  • The directory where output files should be saved.
  • Whether the same root should be used for all output files. Setting this will result in a set of output files that start with the same root, enabling the easy identification of all the files generated from a given FiRePat run. Default is no.
  • The root to be used for all output file names. This can only be specified if the ‘Use same root for all output file names’ box is checked.
  • Whether a log file of the FiRePat run should be recoded. The default is yes. This will record all the input, processing and output parameters, and console messages from the FiRePat program.
  • The name to be used for the log file. This can only be specified if the ‘Use same root for all output file names’ box is unchecked.
  • Whether the correlations should be saved in a csv file. The default is no. This will record the correlations for all sequence pairs where the value is above or equal to the threshold that has been set.
  • The name to be used for the file listing the correlations. This can only be specified if the ‘Use same root for all output file names’ box is unchecked.
  • Whether the local correlations should be saved in a set of csv files, one for each window width. The default is no. This will record the local correlations for all sequence pairs where the value is above or equal to the threshold that has been set.
  • The root name to be used for the files listing the correlations. This can only be specified if the ‘Use same root for all output file names’ box is unchecked.
  • Whether the results should be saved in a csv file. The default is yes.
  • The name to be used for the csv file containing the results. This can only be specified if the ‘Use same root for all output file names’ box is unchecked.
  • Whether the results should be saved in a file in Cytoscape format. The default is yes.
  • The name to be used for the file containing the results in Cytoscape format. This can only be specified if the ‘Use same root for all output file names’ box is unchecked.
  • Whether the results should be saved in html format. The default is yes. The results in this file will be colour coded.
  • The name to be used for the html file containing the colour coded results. This can only be specified if the ‘Use same root for all output file names’ box is unchecked.
  • Whether the results should be saved in latex format. The default is yes. The results in this file will be colour coded.
  • The name to be used for the latex file containing the colour coded results. This can only be specified if the ‘Use same root for all output file names’ box is unchecked.
  • Whether the expression patterns (up, down, same) should be included in the output files. The default is yes.
  • Whether results relating to the first dataset should be first in the output files. The default is yes.
  • Whether the output results should be sorted by the patterns in the first dataset, then the second, (which is the default,) or by the patterns in the second dataset, then the first.
  • The colour to be used in the html and latex output files to indicate an increase in expression level. The default is green.
  • The colour to be used in the html and latex output files to indicate a decrease in expression level. The default is red.

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