Extended Data Fig. 1: A highly parallelized, rapid and storage-efficient pre-processing snakemake pipeline to convert BCL files to ATAC fragment files and RNA sparse matrices.
From: Multiomics and deep learning dissect regulatory syntax in human development
a) Overview of pre-processing workflow. Files are presented in parallelograms while processes are in rectangles. b) Schematic explaining the +4/−4 offset adopted by this pipeline to reach a consensus Tn5 insertion site. c) Definition of a SHARE-seq experiment, samples, nuclei sublibraries, ATAC and RNA sublibraries. Example snakemake configuration file snippets to process sequencing data from mixed experiments. Each experiment should be run in a separate snakemake directory. Detailed pre-processing workflow showing the parallelization behind the scenes for d) ATAC and e) RNA sequencing data.
