docs/analysis/overview-of-analysis-workflow.md

In msk-access/access_data_analysis: ACCESS data analysis

description: Short descriptions on the steps of analysis

Overview of Analysis Workflow

The pipeline aims to generate uniform and useful outputs for analyst in preliminary stage of analysis.

Example command to run through the pipeline:

1. Compile reads

> Rscript R/compile_reads.R -m $PATH/TO/master_file.csv -o $PATH/TO/results_folder

2. Filter calls

> Rscript R/filter_calls.R -m $PATH/TO/master_file.csv -o $PATH/TO/results_folder

3. SV incorporation

> Rscript R/SV_incorporation.R -m $PATH/TO/manifest_file.tsv -o $PATH/TO/results_folder

4. CNA processing

> Rscript R/CNA_processing.R -m $PATH/TO/manifest_file.tsv -o $PATH/TO/results_folder

5. Plot all events

> Rscript R/plot_all_events.R -m $PATH/TO/manifest_file.tsv -o $PATH/TO/results_folder

6. Generate HTML report

msk-access/access_data_analysis documentation built on Nov. 13, 2023, 12:43 p.m.