DdSeeker: a tool for processing Bio-Rad ddSEQ single cell RNA-seq data.

ABSTRACT:

Background

New single-cell isolation technologies are facilitating studies on the transcriptomics of individual cells. Bio-Rad ddSEQ is a droplet-based microfluidic system that, when coupled with downstream Illumina library preparation and sequencing, enables the monitoring of thousands of genes per cell. Sequenced reads show unique features that do not permit the use of freely available tools to perform single cell demultiplexing.

Results

We present ddSeeker, a tool to perform initial processing and quality metrics of reads generated through Bio-Rad ddSEQ/Illumina experiments. Its application to the Illumina test dataset demonstrates that ddSeeker performs better than Illumina BaseSpace software, enabling a higher recovery of valid reads. We also show its utility in the ana

SUBMITTER: Romagnoli D 

PROVIDER: S-EPMC6304778 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature