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

• Published in: BMC genomics Vol. 19; no. 1; pp. 960 - 7
• Main Authors: Romagnoli, Dario, Boccalini, Giulia, Bonechi, Martina, Biagioni, Chiara, Fassan, Paola, Bertorelli, Roberto, De Sanctis, Veronica, Di Leo, Angelo, Migliaccio, Ilenia, Malorni, Luca, Benelli, Matteo
• Format: Journal Article
• Language: English
• Published: London BioMed Central 24.12.2018; BioMed Central Ltd; BMC
• Subjects: Algorithms; Animal Genetics and Genomics; Bioinformatics; Biomedical and Life Sciences; Breast cancer; Computational Biology; Data processing; Datasets; Demultiplexing; Experiments; Gene Expression Profiling; Gene sequencing; Genomes; Genomics; Life Sciences; Microarrays; Microbial Genetics and Genomics; Microfluidics; Plant Genetics and Genomics; Proteomics; Ribonucleic acid; RNA; RNA - genetics; RNA sequencing; scRNA-seq; Sequence Analysis, RNA; Single-Cell Analysis - methods; Single-cell transcriptomics; Software; Source code; Transcription factors; Transcriptome - genetics; Transcriptomic methods; Single-cell transcriptomics; Bioinformatics; scRNA-seq
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-018-5249-x

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 analysis of an in-house dataset including two read sets characterized by low and high sequencing quality. ddSeeker and its source code are available at https://github.com/cgplab/ddSeeker . Conclusions ddSeeker is a freely available tool to perform initial processing and quality metrics of reads generated through Bio-Rad ddSEQ/Illumina single cell transcriptomic experiments.