What is the output of CeleScope?Home FAQ Bioinformatics CeleScope What is the output of CeleScope?The main output files of CeleScope are:HTML QC report, including the main metrics for: sequencing, demultiplexing, trimming, alignment to reference genome, annotation and cell calling.Count matrix: file containing the transcript (UMI) counts for every gene and barcode corresponding to a cell in the cell calling.