Fast analysis of scATAC-seq data using a predefined set of genomic regions.

ABSTRACT: Background: Analysis of scATAC-seq data has been recently scaled to thousands of cells. While processing of other types of single cell data was boosted by the implementation of alignment-free techniques, pipelines available to process scATAC-seq data still require large computational resources. We propose here an approach based on pseudoalignment, which reduces the execution times and hardware needs at little cost for precision. Methods: Public data for 10k PBMC were downloaded from 10x Genomics web site. Reads were aligned to various references derived from DNase I Hypersensitive Sites (DHS) using kallisto and quantified with bustools. We compared our results with the ones publicly available derived by cellranger-atac. We subsequently tested our approach

SUBMITTER: Giansanti V 

PROVIDER: S-EPMC7308914 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature