ROIs enable a new way of visualizing, characterizing, and analyzing aligned sequence data from next generation sequencing (NGS) experiments that will have implications on the quality control as well the biological interpretation of such experiments. By decoupling the strict linear order that is implied by the reference genome we allow for a much more detailed analysis of the alignment results than it was previously possible. We show this on two examples: one from the quality control angle where we identify and characterize regions with coverage profiles that can most certainly be associated to technical artefacts, and one example where our method can help or even guide the interpretation of miRNA data. Though we restricted ourselves to these two example for reasons of brevity the potential of this method is much broader and can be applied to CHiPSeq, RNASeq, transcription start site analysis and potentially many more biological problems. This technology can also help understanding the technical biases imposed on the experiments by the instruments and protocols.
The region of interest (ROI) file format is a text based format that is compatible with the BED6 file format. Thus, columns are separated by the tabulator character and the first four columns describe the location of the region and a name. We use the length of the region in lieu of the score, which is followed by the strand (+/-). What follows is an arbitrary but consistent (within the file) number of numerical columns (metrics), followed by a comma separated list of integer values (usually coverage values).
The file format allows for comment lines, which have “#” as the first character. By convention, in the file header a single line starting with “##” contains column names.
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input file
name of the input file

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Table with ROI information

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