ZUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs.

ABSTRACT:

Background

Single-cell RNA-sequencing (scRNA-seq) experiments typically analyze hundreds or thousands of cells after amplification of the cDNA. The high throughput is made possible by the early introduction of sample-specific bar codes (BCs), and the amplification bias is alleviated by unique molecular identifiers (UMIs). Thus, the ideal analysis pipeline for scRNA-seq data needs to efficiently tabulate reads according to both BC and UMI.

Findings

zUMIs is a pipeline that can handle both known and random BCs and also efficiently collapse UMIs, either just for exon mapping reads or for both exon and intron mapping reads. If BC annotation is missing, zUMIs can accurately detect intact cells from the distribution of sequencing reads. Another unique feature of zUMIs is the adapt

SUBMITTER: Parekh S 

PROVIDER: S-EPMC6007394 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature