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03 - Initial QC

Created: 2022/08/10 15:30:51 Last modified: 2022/08/24 17:12:04

  • Aim: This document documents/describes initial QC for this project
  • Prerequisite software: slurm v20.11.6, singularity v3.7.2-1.el7, GNU coreutils
  • OS: ORAC (CentOS Linux) (ESR production network)

Table of contents

Merge initial sequencing summary reports

The initial sequencing summary reports are in two files, but are actually from the same sample and run, therefore we will merge them for downstream QC

Run bash script to merge the initial sequencing summary reports. See my script at ./scripts/03_initial_qc/01_merge_summary_reports.sh

sbatch ./scripts/03_initial_qc/01_merge_summary_reports.sh

pycoQC

Run bash script to get the run pycoQC. See my script at ./scripts/03_initial_qc/02_pycoqc.sh

sbatch ./scripts/03_initial_qc/02_pycoqc.sh