Raw Detections

The Single molecule analysis with the sm-analysis program pipeline produces a so-called raw detections report also informally called own output.

The raw detections file contains, as the name suggests, raw data coming directly from the ipdSummary program. That data is used by sm-analysis to produce the methylation report, which is a detailed view (per molecule) of the methylation status of individual molecules for each GATC in that molecule.

The raw detections file is a CSV file. Each line in this file corresponds to an individual detection. Its format used by described in pacbio_data_processing.sm_analysis.add_to_own_output()