Recipe: Analyzing RNA-Seq data with adapter sequences using Galaxy
9 videos • 4,099 views • by GenomeSpace This Recipe provides an outline of one method to preprocess and determine the quality of RNA-Seq libraries. Given a set of raw RNA-Seq reads, the goal is to align the reads to a reference genome and assess the quality of the read alignments by obtaining metrics such as depth of coverage, rRNA contamination, continuity of coverage, and GC bias. The purpose of this Recipe is to process raw RNA-Seq reads prior to aligning them against a reference genome. In particular, this recipe uses a dataset which has RNA-Seq reads contaminated with adapter sequences. First we identify and remove adapter sequences using Galaxy, then we process the data and align it to a reference genome using GenePattern.