Benchmarking references for functional genomics

This repo contains the code used in performing the study.

Compute

Two compute systems were used in this study. The WashU HTCF and WashU Compute1 systems. HTCF is a slurm based system. Compute1 is a docker based system using LSF for job submission.

Workflows/Code

• ATAC-seq: AIAP
• RNA-seq: bulk-rna
• Hi-C: hic
• WGBS: https://github.com/xzhuo/wgbs/tree/fan-branch
• Post-processing analysis
  • Read tracing: Read_Tracing
  • QC analysis:
    • Plot_Metrics.Rmd
    • PlotMetrics.R
    • Plot_Metrics_and_Outputs.Rmd
    • PlotMetrics.R
  • Functional estimate analysis
    • ComparePeaks.Rmd
    • CompareExpressionByStrategy.Rmd
    • Compare_LinearOnly_Latest.R
• Variant enrichment analysis
  • HPRC_DV_Enrichment
  • HPRC_SV_Enrichment
  • Pangenome_structure_diversity
• Overrepresentation analysis
  • ORA
• Liftover
  • Liftover

Processed Data files

• ATAC-seq:
  • https://wangftp.wustl.edu/~jmacias/HPRC_ATACseq/
  • https://wangftp.wustl.edu/~jmacias/ATACseq_Pangenome/
• RNA-seq:
  • https://wangftp.wustl.edu/~jmacias/HPRC_RNAseq/
  • https://wangftp.wustl.edu/~jmacias/HPRC_RNAseq_Pangenome/
• WGBS:
  • https://wangftp.wustl.edu/~jmacias/HPRC_WGBS/
• Hi-C:
  • https://wangftp.wustl.edu/~jmacias/HPRC_HiC/

Epigenome browser session files