/Mangrove_PlantParts_MG

Primary LanguageShell

Singapore Mangrove Transplants

Looking for differences in C genes between sediment, pneumatophore, and leaf samples

Sampling done at Chek Jawa and Semaku

- 2 sites
- 10 trees at each site
- Sediment, Pneumatophore, and Leaf samples taken at each tree
- N=60 units

60 samples sequenced on a full Illumina NovaSeq run.

Workflow

  1. QC with fastqc
  2. Assembly with metaSPADEs
  3. Gene prediction with metaeuk (database)
  4. KO assignment with kofamscan
  5. Gene Ontology and PFam terms attached with custom scripts
    • Bash scripts for reference. Need to adjust file paths to match new structure and local machines