Quick Start

  1. Ensure your O2 environment is properly setup to run bcbio.
  2. Put your data in permanent storage and create a copy on /n/scratch2/.
  3. Do you have multiple fastq files that need to be merged for each sample?
    • If yes, run bcbio_prepare_samples.py to merge the files. Rename the resulting *-merged.csv to alignment.csv. (This is often the case for deep RNAseq experiments.)
    • If not, compose alignment.csv that maps filenames to corresponding sample descriptions. (This is often the case for DGE.)
  4. (Optional) Download the latest human (or mouse) genome reference.
  5. Compose a setting YAML file.
  6. Instantiate the bcbio workspace. Descend into alignment/work subdirectory. Kick off a bcbio run.