What input files are required to run the CeleSCOPE data analysis pipeline?

The input files for CeleSCOPE^® are:

• Sequencing FASTQ files.
• Reference genome FASTA file.
• Reference genome annotation GTF file.

The FASTA and GTF files need to be indexed as mentioned on the CeleSCOPE GitHub page.

CeleSCOPE is Singleron’s bioinformatics analysis pipeline designed to process raw sequencing data generated using Singleron’s single cell technologies. It converts raw sequencing data (FASTQ files) into gene expression matrices that can be used for downstream single cell analysis. CeleSCOPE performs several key processing steps, including cell barcode identification, UMI processing, read alignment, gene quantification, and cell calling.

The resulting gene expression matrices can then be imported into CeleLens™, Singleron’s interactive analysis platform, for downstream analysis, including clustering, visualization, differential gene expression analysis, and cell-type annotation.