Which RNA-Seq Processing Algorithm Should I Pick? A Comparison of RNA-Seq Pipelines Based on Experimental Design, Sample Properties and Sequencing Technology

摘要

In the past few years, the dramatic increase in sequencing throughput has been paralleled by a proliferation of bioinformatic tools designed to analyze and quantitate next generation sequencing data. In the case of RNA-Seq, a number of analysis packages have been developed, but whether some might be better suited to the analysis of samples within different ranges of read coverage or RNA quality has not been extensively studied. Here, we evaluated head-to-head eight different packages on single-end- and paired-end-RNA-Seq data at different read coverages. Gene expression and alternative splicing were quantitated and compared across the different methods using standard accuracy and precision metrics. We demonstrate critical differences in how the different algorithms are able to handle different read lengths and read coverage levels and how these changes impact gene expression and isoform usage values. Articles from Journal of Biomolecular Techniques : JBT are provided here courtesy of The Association of Biomolecular Resource Facilities.