Output Description

One of the strengths of RAPID is that a number of useful files with statistics and plots are automatically created, which can be used for additional analysis.


An output folder is created, for each annotation BED file supplied in rapidStats analysis, with the following files:

  • Statistics.dat - A tab-separated file that contains a number of statistics for each region including read counts, number of read modifications, nucleotide specific read modifications, and strand and length specific read counts.
  • TotalReads.dat : Lists the total number of reads mapped to the genome (given by parameter -i and excluding reads that may have mapped to the contamination file)
  • Other associated files used for calculation and reporting. * alignedReads.sub.compact has the compact information of aligned reads. If intermediate files are not removed, aligned BAM files will be present.


In each folder created by rapidNorm analysis exist the following files:

  • NormalizedValues.dat - A tab-separated file that contains the actual and normalized values for each region/sample provided in the config file.
  • Other associated files used for calculation and reporting.


RapidVis output description when ran in two different modes.

  • stats

    FolderName.html - An automatically generated main HTML file which is an ensemble of individual gene/region’s HTML files that contain different plots analyzing read counts, distribution of reads on the two DNA strands and listing smallRNA modifications stratified by the defined regions.

  • compare

    FolderName.html - An automatically generated HTML file consisting of various plots like read lengths, antisense ratio, etc. in different scales, compared across all the samples.

More description about each plot can be found in UseCases.

Differential Analysis

In each folder created by rapidDiff analysis exist the following files:

  • DiffExp_Statistics.csv - A CSV file containing the normal counts retrieved for each sample and the DESeq2 statistics obtained
  • DiffExp_Plots.pdf - A PDF file containing MA-Plot, Heatmap of top ‘n’ q-values, PCA plot of the samples analysed