asSeq: A set of tools for the study of allele-specific RNA-seq data

RNA-seq has become one of the major solutions for genome-wide inquiry of transcriptome variation. Allelespecific expression (ASE), which can be measured by RNA-seq but not by traditional microarray, provides a new perspective of transcriptome variation. Allelic imbalance of gene expression may be due to cis-acting genetic variant or parent-of-origin regulation. Currently this R package asSeq only provides support for assessing cis-acting eQTL. Later we will include another set of functions that can dissect (cis-acting) genetic effect and parent-of-origin effect. Here cis-acting regulation means a genetic variant on one allele (i.e., the maternal or paternal allele) only affects the expression on the same allele. A cis-eQTL often refers to a localeQTL. In this document, we use a more precise definition of cis-eQTL such that they are the eQTL associated with ASE. Interested readers are referred to Sun (2102) [1] and Sun and Hu (2012) [2] for more details. Sun (2102) [1] provides the details of a statistical method for eQT mapping using both total expression and ASE. Sun and Hu (2012) [2] is a review paper that reviews topics related with eQTL mapping using ASE or isoform-specific expression. In addition to main functions for eQTL mapping using total expression or ASE, asSeq also provides utility functions for quality control or extracting allele-specific RNA-seq reads, which are the RNA-seq reads that overlap with heterozygous genetic markers. Figure 1 shows a complete pipeline of eQTL mapping using ASE. Some additional scripts are provided for certain steps of this pipeline.