${{\color{Black}\Huge{\textsf{Routine Codes and Pipelines}}}}$

Compilation of codes and pipelines used routinely in the lab

${{\color{Black}\normalsize{\textsf{Epigenetics, 3D Genome, and Functional Annotation}}}}$

${{\color{Green}\Huge{\textsf{Overview}}}}$

This repository is a curated collection of computational scripts and pipelines regularly utilized in the Hawkins Lab for genome-wide studies. It provides essential tools for analyzing histone modifications, DNA methylation, 3D genome organization, and the annotation of coding and non-coding RNAs, reflecting the lab's commitment to advancing gene regulation and functional genomics research.

• Applications
  
• Functional annotation of genomic regions and chromatin states.
  
• Characterization of gene regulatory landscapes in various cellular contexts.
  
• 3D genome structure analysis for insights into chromatin organization and its role in gene expression.
  

🔶 Contents:

Demultiplexing NGS libraries Best Practices

• create a sample ID label to sample sheet files Ex: library.name-Tissue.or.Cells-animal.ID-assay-run.date
  
• $${\color{purple}T01-muscle-01-ATAC240101}$$
  

• bcl2fastq demultiplexing NGS libraries (convert *.bcl to *.fastq files)
  🔗 https://github.com/hawkinslab226/Routine_pipelines/blob/main/demultiplex_libraries_hawkinslab.sh

Normalization raw counts

🔗 https://github.com/hawkinslab226/Routine_pipelines/blob/main/RPKM_norm.R