qcmeng / onion_bsa_rnaseq_workflow

Workflow for Analysis of Onion Bulked Segregant Analysis RNASEQ

Workflow for BSA-RNASEQ analysis targetting onion AcBlt1 locus and other QTL affecting Bolting (precocious flowering)##

Each directory is a discrete step in the analysis

Reproducible workflows docuemnted in 3 ways:

1. Unix shell workflows originally created using the MOA Command-line Bioinformatics framework. See http://moa.readthedocs.org/en/latest/index.html. Most steps are unix shell commands (MOA 'simple' template) visible in the .moa/config file. These are executed in order precommand -> process -> postcommand. Equivalent shell scripts provided as run.sh
2. R Markdown as Rmd files
3. iPython notebooks

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Citation

Validation of Variants Identified in PoolSeq by Optimised High Resolution Melting Assay Design

S. Baldwin, S Thomson, M Pither-Joyce, K Wright, R Macknight, S Lui, B Warren, Z Dwight, J McCallum

in preparation

New Zealand Institue for PLant and Food Research 2014