FiRePat input data
FiRePat requires the user to tell the software where to find the two files containing the input data. For each data file the user can specify what type of data it contains and whether it has a header row. By default, it is assumed that no header row is present, the first dataset is assumed to be sRNA data and the second non-sRNA data. A name is required for each dataset, this will be used to identify it in the output files, by default the names of the two datasets are first and second ‘First’ and ‘Second’.
The user must also specify how may samples there are and how many replicates there are. By default the number of replicates is 1, i.e. there are no replicates.
N.B. the two input datasets must be in comma separated values (csv) format where columns represent samples and rows represent individual sequences. The two input files must match exactly in terms of sample order, number of replicates per sample and order of replicates. The same number of replicates must be present for each sample and the replicates for each sample must be grouped together. The first column must contain the unique identifier for each sequence. The first row can be a header row (which will be ignored for the analysis) or it can be the first sequence.
Finally, the user must enter the names of the samples, or specify that sequential sample names should be generated from a common root.