Requirements: Perl for the pipeline. Java and MySQL to build the database and view the results.
Reference: C. Soderlund, W. Nelson, and S. Goff. (2014) Allele Workbench: transcriptome pipeline and interactive graphics for allele specific expression. PLoS ONE
Description: The Allele Workbench (AW) is for the analysis of allele-specific expression. The pipeline has been tested on Linux, and the Java code has been tested on Linux and MacOSX. It does not work with MySQL V8.
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.
Release v1.1 beta: (1) Improved error catching and trace output. (2) Speedups. (3) Runs with MariaDB v10.4.7.