The University of Arizona
AW User Guide
AGCoL | AW Home | AW Guide v1.0 | Tour
The documentation consists of three parts:
Pipeline Running the pipeline.
Files File formats and naming convensions.
runAW Building the AW database

The runAW interface has the above three documentations available from it.

To query and view the database, just type: viewAW <database name>.

The viewAW interface has "Help" on every display page.

References

Pipeline:
  1. FastQC: A quality control tool for high throughput sequence data. [bioinformatics.babraham.ac.uk/projects/fastqc]
  2. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics.
  3. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111.
  4. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
  5. Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
  6. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29: 15-21.
  7. Roberts A, Pachter L (2013) Streaming fragment assignment for real-time analysis of sequencing experiments. Nat Methods 10: 71-73.
runAW: the output of the following software can be input for variant effects.
  1. Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 6: 80-92.
  2. McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F (2010) Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26: 2069-2070.
Email Comments To: tcw@agcol.arizona.edu