Integrating long read RNA-seq data into BioConductor workflows with NanoporeRNASeq
Yuk Kei Wan,Ying Chen,Jonathan Goeke Genome Institute of Singapore
Abstract
The NanoporeRNASeq package is the first long-read RNA-seq ExperimentData package available on Bioconductor. The data was generated from Oxford Nanopore Sequencing and consists of six samples from two human cell lines, namely K562 and MCF7, each with three replicates (one from direct RNA sequencing and two from direct cDNA sequencing). The six samples in this package are aligned to chromosome 22 (Grch38) in bam file format and are a subset of samples from the Singapore Nanopore Expression Consortium (SG-NEx), which provides comprehensively benchmarked datasets from three Nanopore long-read RNA-seq protocols (direct RNA, direct cDNA, and PCR cDNA) being run on five cancer cell lines (A549, Hct116, HepG2, K562, and MCF7). The NanoporeRNASeq package can be used for illustrating and evaluating Bioconductor workflows for transcript discovery, quantification, and differential expression analysis of long-read Nanopore RNA-seq.
Keywords: long-read RNA sequencing,nanopore RNA sequencing,transcriptomics,transcript discovery and quantification