Analyses for paper "Differential Expression on Publicly Available RNA-Seq Datasets Using Phylogenetic Comparative Methods to Understand Nickel Accumulation in Plants"

• Folder OGs-modelplants: Contains all scripts and open source code from external softwares (see Dependencies file) needed to built and annotate orthologs groups .

  • input: fasta formatted proteomes, swissprot database, metacyc database
  • output: fasta formatted orthologs groups, flat files of groups numbers with associated annotations (putative functions, EC numbers and Gene Onthology entries)

• Folder OGs-nickelplants : contains the scripts needed to enriched the orthologous groups built from model plants (see OGs-modelplants) with putative proteins translated from de novo transcriptomes.

  • inputs : transcriptome (fasta formatted contigs from de novo assemblies)
  • output : a list of peptide length, contig name, ortholog group number

• Folder differential-expression-analysis : contains everything needed to perform differential analysis

  • inputs : the expression table for each sample, metadata for each sample, list of contigs and associated OG number for all species, phylogenetic tree
  • output : list of DE OGs, figures