What is the output of CeleScope?Home FAQ Bioinformatics BI Software and Data Analysis What is the output of CeleScope?The main output files of CeleScope are:An HTML QC report, including the main metrics for: sequencing, demultiplexing, trimming, alignment to reference genome, annotation and cell calling.A count matrix, with the transcript (UMI) counts for every gene and every barcode that was recognized as a cell in cell calling.