Read alignment is a common process applied to high-throughput sequencing data, being one of the first stages required for many different types of analysis. In the RNA-Seq scenario, this process is used to quantify gene expression. The goal of the read alignment is to map short sequencing reads efficiently to a large reference genome to identify the 'correct' genomic loci from which the read originated whilst taking into account errors in the sequence reads. This functionality can be found under transcriptomics → RNA-Seq Alignments.
Two alignment strategies are available:
STAR: STAR is a gapped RNA-Seq read mapper, with support for splice-junction and fusion read detection, and it was designed to align non-contiguous sequences directly to a reference genome.
BWA: BWA is a software package for mapping low-divergent sequences against a large reference genome. Since BWA is an ungapped mapper, this option is recommended to analyze data from simpler species such as bacterias.