The University of Arizona
AW: Allele Workbench
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This project is funded in part by National Science Foundation grants DBI-1265383 and IOS-1248090.

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 contains:

  1. 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.
  2. 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.
  3. viewAW is a Java interface to view the database.
Download
  AW Pipeline and demo files
  AW Java and demo files
  Source code
 
Documentation
  AW Tour
  AW User Guide
  Release (26Jan15)
 
Java AW applet
  Demo - in release package
  Mouse - published
 
Heterosis study
  Mouse
 
References
C. Soderlund, W. Nelson, and S. Goff. (2014) Allele Workbench: transcriptome pipeline and interactive graphics for allele specific expression. PLoS ONE Link
runAW
viewAW overview
viewAW query
viewAW table
Click an image to view closeup

NSF Disclaimer

Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Email Comments To: tcw@agcol.arizona.edu