wf-single-cell | following single-cell kits | Genomics library

The workflow uses nextflow to manage compute and software resources, as such nextflow will need to be installed before attempting to run the workflow. The workflow can currently be run using either Docker or singularity to provide isolation of the required software. Both methods are automated out-of-the-box provided either docker or singularity is installed. It is not required to clone or download the git repository in order to run the workflow. For more information on running EPI2ME Labs workflows visit out website.
fastq: A fastq file or directory containing fastq input files or directories of input files.
ref_genome_dir The path to the 10x reference genome directory (see Downloading reference data below)
10x sample metadata using either: The following parameters, which are applied to all samples (the default): kit_name options: 3prime (default), 5prime, multiome kit_version 3prime options: v2, v3 (default) 5prime options: v1 multiome options: v1 expected_cells [500]
plot_umaps: This flag controls whether UMAP projections are generated and dispalyed in the report (default false). If UMAP output is required apply like: --plot_umaps. or single_cell_sample_sheet (not to be confused with the optional MinKNOW sample_sheet) allowing per sample configuration.
configs.stats.json: provides a summary of sequencing statistics and observed read configurations, such as n_reads: number of total reads in the input fastq(s) rl_mean: mean read length n_fl: total number of reads with the read1-->TSO or TSO'-->read1' adapter configuration (i.e. full-length reads) n_plus: number of reads with the read1-->TSO configuration n_minus: number of reads with the TSO'-->read1' configuration
bams: Folder of bam alignment files where each alignment contains the following sequence tags CB: corrected cell barcode sequence CR: uncorrected cell barcode sequence CY: Phred quality scores of the uncorrected cell barcode sequence UB: corrected UMI sequence UR: uncorrected UMI sequence UY: Phred quality scores of the uncorrected UMI sequence The bam files are output per chromosome (default) unless --merge_bam is set.
gene_expression.processed.tsv: TSV containing the gene (rows) x cell (columns) expression matrix, processed and normalized according to:
matrix_min_genes: cells with fewer than this number of expressed genes will be removed
matrix_min_cells: genes present in fewer than this number of cells will be removed
matrix_max_mito: cells with more than this percentage of counts belonging to mitochondrial genes will be removed
matrix_norm_count: normalize all cells to this number of total counts per cell
transcript_matrix_processed.tsv: TSV containing the transcript (rows) x cell (columns) expression matrix, processed and normalized in the same manner as the genes. These expression values are determined by first generating a transcriptome per sample using stringtie and then assigning reads to transcripts aligning them to this transcriptome with minimap2. Only reads that map unambiguously to a reference transcript are assigned. The assembled transcripts with the following gffcompare class codes are excluded: i, p, s or u. See the gffcompare and this image, and only cells and genes that pass the gene filtering described above are included.
read_tags.tsv: TSV file witjh the following columns: read_id gene (assigned gene) transcript (assigned transcript id) barcode (corrected barcode) umi )corrected umi