NOTES

Tips and Tricks

1. Quality Thresholds:
   - Start with a quality threshold of 20 when trimming reads. Adjust based on QC reports to balance read retention and quality.

2. Sample Naming:
   - Use consistent and descriptive filenames for your FASTQ files to easily track samples throughout the pipeline.

3. Reference Genome:
   - Ensure that the reference genome and annotation files match (e.g., version and species) to avoid alignment and counting errors.

4. Parallel Processing:
   - Utilize multiple threads (`nthreads`) in alignment and quantification steps to speed up processing, especially on multi-core systems.

5. Error Checking:
   - After each step, verify the output files exist and contain expected data to catch issues early.

6. Visualization:
   - Always visualize QC reports and normalized counts to ensure data integrity before proceeding to the next steps.

7. Backup Configuration:
   - Keep a separate configuration file for parameters like directories and thresholds to easily modify settings without altering scripts.

8. Documentation:
   - Comment your scripts clearly to remember the purpose of each section, making it easier for others (and future you) to understand the workflow.

9. Modular Scripts:
   - Keep scripts modular to allow running specific steps independently, facilitating troubleshooting and flexible analyses.

10. Regular Updates:
    - Periodically update your packages and reference data to incorporate the latest improvements and annotations.

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