The goal of many RNA sequencing projects is to determine how genes are differentially expressed between experimental groups. With the ever-decreasing cost of sequencing and increasing flowcell capacities, processing large amounts of RNA-seq data can require vast computational resources not readily available to the average researcher and may hinder researchers from starting their analyses.
We offer two levels of RNA analysis packages, Basic and Intermediate, which can help our customers start analyzing their differential expression studies. These standard packages can be a great starting place for burgeoning bioinformaticians, but they will not pick up non-coding RNA and are not intended for metatranscriptomes.
Basic RNA Analysis
The first level of analysis we offer, Basic Analysis, maps RNA sequencing reads to a provided annotated reference genome. Read mapping and counting can be computationally expensive, so this package is ideal for customers who wish to perform their own comparisons and more in-depth analysis, but may lack the computational resources necessary to produce the raw counts in a reasonable amount of time.
Raw counts are returned in table format, with multi-mapping reads discarded. Examples of methods can be found here for prokaryotic samples and here for eukaryotic samples. For experiments with multiple organisms, we standardly recommend performing independent mapping for each organism.