NLDMseq

NLDMseq is a software tool designed to accurately measure gene and isoform expression from RNA-Seq data. The tool addresses the difficulties of ambiguous reads mapping to reference transcriptome caused by alternative splicing and non-uniformity of read distribution along the reference transcriptome.

The NLDMseq method employs latent variables to model the unknown isoforms, which helps identify the underlying percentage of multiple spliced variants. The isoform- and exon-specific read sequencing biases are also modeled to account for the non-uniformity of read distribution. They are identified by utilizing the replicate information of multiple lanes of a single library run.

The proposed method provides an approach to accurately estimate gene and isoform expression from RNA-Seq data by modeling the isoform- and exon-specific read sequencing biases. It uses a latent variable model to discover the hidden pattern of read sequencing. The NLDMseq method has been shown to work well in both simulations and real datasets and has competitive performance compared to popular methods. The tool is helpful in the downstream analysis of differential expression. The NLDMseq method makes bias corrections based on surrounding sequence content and gene- and isoform-specific biases, as revealed by recent studies.