Instructional Tutorial for Using Demuxlet V1

Genetic multiplexing of barcoded single cell RNA-seq Introduction demuxlet is a software tool to deconvolute sample identity and identify multiplets when multiple samples are pooled by barcoded single cell sequencing.demuxlet takes (1) a SAM/BAM/CRAM file produced by the standard 10x sequencing platform, or any other barcoded single cell RNA-seq (with proper --tag-UMI and --tag-group) options (2) a VCF/BCF file containing the genotype (GT), posterior probability (GP), or genotype likelihood (GL) to assign each barcode to a specific sample (or a pair of samples) in the VCF file. Tutorial for demuxlet This tutorial provides streamlined instructions for using the tool demuxlet. For a more detailed description of all of the options available to use with demuxlet, please refer to the README (attached in .zip file). demuxlet has several dependencies and this tutorial provides steps to use a docker instance to minimize compatibility issues and an alternative of installing demuxlet from source. demuxlet is a software tool to deconvolute sample identity and identify multiplets when multiple samples are pooled by barcoded single cell sequencing. demuxlet requires the following input files: a SAM/BAM/CRAM file produced by the standard 10x sequencing platform, or any other barcoded single cell RNA-seq (with proper --tag-UMI and --tag-group) options. a VCF/BCF file containing the genotype (GT), posterior probability (GP), or genotype likelihood (GL) to assign each barcode to a specific sample (or a pair of samples) in the VCF file.