02 Working Directory

Working Directory

Summary

PROJECT
├── data
├── results
├── scripts
├── references
├── notebooks
├── docs
├── site
├── log
├── README.md
└── .gitignore

Folders

PROJECT
├── data
│   ├── external
│   └── processed
├── results
│   ├── assay_fcc
│   ├── assay_hic
│   └── region
├── scripts
├── references
├── notebooks
├── docs
├── site
├── log
├── README.md
└── .gitignore

Naming Convention of folders and files

Below are some naming convention in this documentation.

  • Assay folder name
    • <Assay Type>_<Cell Type>_<Lab>_<Label>
    • Label
      • batch, source, people, id numbers
STARR_ATAC_K562_Reddy_KS91
STARR_ATAC_K562_Reddy_KS274
STARR_ATAC_K562_Reddy_KSMerge
STARR_WHG_K562_Reddy_A001
MPRA_Tiling_K562_Tewhey_Hannah
MPRA_Lenti_K562_Nadav_Vikram
CRISPRi_FlowFISH_K562_Riley_JinWoo
CRISPRi_Growth_K562_Gersbach_JinWoo
CRISPRi_Growth_K562_Gersbach_Alex
  • Assay file name
    • <Prefix>.<Genome>.<Input/Output/Log2FC/ZScore>.<Replicate>.<Region>.<Unstranded/Stranded>.<File Extension>
    • Prefix
      • ASTARRseq_K562_KS91
      • WSTARRseq_K562_A001
      • TMPRA_K562_OL13
      • TMPRA_K562_OL43
      • TMPRA_K562_OL45
      • TMPRA_K562_Merge
      • LMPRA_K562
      • CRISPRi_HCRFF_K562
      • CRISPRi_Growth_K562
    • Replicate
      • rep1/2/3/4
      • rep1_vs_rep2
      • rep_all
    • Region
      • WHG = whole genome
      • MYC = MYC region
      • GATA1 = GATA1 region
      • Chrom_Main = chr1-22,X,Y
      • Chrom_Auto = chr1-22 (Autosome)
      • Chrom_Sex = chrX,Y (Sex chromsome)
  • ENCODE region file name
    • <Prefix>.<Genome>.<Experiment ID>.<File ID>.<Assay>.<Description>.<File Extension>
    • Prefix: biosample
      • K562: a human erythroleukemic cell line
      • A549: a human lung epithelial Cell line
      • Hsa: Human
    • Genome: reference for alignment
      • hg38: GRCh38
      • hg19: GRCh37
    • Assay and Description
      • ATAC/DNase
      • ChIPseq.H3K27ac
      • cCREs/ChromHMM
  • Enhancer calls