Adam Roberts
University of California, Berkeley (UC Berkeley)
Computer Science

eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences. In this talk I will focus on the application to transcript-level RNA-Seq quantification. The method is based on an online-EM algorithm that results in space (memory) requirements proportional to the total size of the target sequences and time requirements that are proportional to the number of sampled fragments. I'll show that eXpress can accurately quantify much larger samples than other currently available tools while greatly reducing computing infrastructure requirements. eXpress can also be used to build lightweight high-throughput sequencing processing pipelines when coupled with a streaming aligner, as output can be piped directly into eXpress, effectively eliminating the need to store read alignments in either memory or disk. This is joint work with Lior Pachter.

Presentation (PDF File)

Back to Workshop II: Transcriptomics and Epigenomics