Differential Gene Expression Analyses on Selaginella

The Script SelaginellaPipeline.sh has all (or probably most) of the commands to do the following:

• Run Transdecoder to extract coding sequences from Trinity contigs
• Run an all-by-all blastp analysis of amino acid translations
• Map reads to Trinity contigs keeping all alignments
• Run Corset to cluster contigs
• Create MySQL database with contigs, blast results and Corset results
• Extract sequence from each Corset cluster with highest blast hit and write to file
• Run OrthoMCL on highest scoring sequences and add results to database
• Use count data from Corset to run differential expression analyses using DESeq and DGEclust
• Make trees for each gene family and map on expression data

• Blast+ (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/)
• Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
• Corset (https://code.google.com/p/corset-project/)
• DESeq (http://bioconductor.org/packages/release/bioc/html/DESeq.html)
• DGEClust (http://dvav.me/dgeclust/)
• ETE2 (http://etetoolkit.org/)
• MAFFT (http://mafft.cbrc.jp/alignment/software/)
• MySQL (http://www.mysql.com/)
• OrthoMCL (http://www.orthomcl.org/orthomcl/)
• PhyML (http://atgc.lirmm.fr/phyml/)
• R (http://www.r-project.org/)
• Transdecoder (http://transdecoder.sourceforge.net/)
• Trinity (http://trinityrnaseq.sourceforge.net/)

Adaptor sequence and low quality base pairs were trimmed using the fastq-mcf utility from ea-utils {eautilsCommand:6tDggvj9} using a quality threshold of 10.