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Snakemake RNA modification regression pipeline

Snakemake pipeline for performing regression in RNA modification data

Quickstart

Quick demo shown below.

  1. Set up conda environments shown in envs.
# Starting from this directory
SNK_REPO=$(pwd)

cd envs

# Option 1: direct conda
bash environment_setup.sh

# Option 2: docker (use if running on mac M*)
docker build -t rna_mod_gsis --platform linux/amd64 .
  1. Run demo
# Starting from this directory
SNK_REPO=$(pwd)

# set up the directory with the required data dir
cd demo
ln -s data/demo_data/demo_data-random1k.h5ad data/data.h5ad

# Run analysis
bash run_gwas__local_docker.sh

Working directory structure

  • Required input files: in the data directory.
  • Final output data: in the results directory.
  • Logs of all jobs: in the logs directory.

Input

AnnData .h5 file with the following attributes:

  • Layers contains those specified under left hand side of formula configuration. Example: counts_modified and counts_unmodified in the demo dataset
  • Observation slot (.obs) contains columns specified on right hand side of formula configuration. Example: glucose_condition, cell_type, and library_size in the demo dataset
  • X slot contains total counts of the two test layers. Example: X contains counts_modified + counts_unmodified in the demo dataset