Description: The Allele Workbench (AW) is for the analysis of allele-specific expression.

Download Pipeline.tar.gz: http://www.agcol.arizona.edu/software/aw. This contains the pipeline perl scripts, external programs and pipeline demo files.

Download AW_1_1.tar.gz: https://github.com/csoderlund/AW/releases. This contains the Java code and interface demo files.

Documentation: https://csoderlund.github.io/AW.

Requirements: Perl for the pipeline. Java and MySQL to build the database and view the results. The pipeline has been tested on Linux, and the Java code has been tested on Linux and MacOS.

Reference: C. Soderlund, W. Nelson, and S. Goff. (2014) Allele Workbench: transcriptome pipeline and interactive graphics for allele specific expression. PLoS ONE

The package contains:

Pipeline specific to F1 hybrid (inbred) RNA-seq data. Input: RNA-seq from one or more libraries (optional replicas), the genome sequence to align to, the gene annotation file, and an optional VCF variant file. Output: The heterozygous SNPs. Optionally, it can also output the VCF file and transcript heterozygous read counts.

runAW is a Java interface to build the database. Input: The gene annotation file, genome sequence, VCF file and heterozygous SNP file. Optionally, it can take as input variant effects, NCBI annotation and transcript heterozygous read counts. Compute: Allele Imbalance (AI) is computed for both the heterozygous SNP coverage and heterozygous transcript read counts. If effects are not loaded, a subset are computed. The parental spliced transcripts and protein sequences are computed. Other various supporting information and summary statistics. Output: the AW database along with files of the parental spliced transcripts and protein sequences.

viewAW is a Java interface to query view the results.