11 Prepare: FCC

Results after preparation

  • Process files in data (arrange/extract)
  • SymLink files in data (file aliases)

FCC assay

PROJECT/results/assay_fcc
├── STARR_ATAC_K562_Reddy_KS91
│   ├── fragment_counts
│   │   ├── ASTARRseq_K562_KS91.hg38.Input.rep1.WGS.unstranded.bed.gz
│   │   ├── ASTARRseq_K562_KS91.hg38.Input.rep2.WGS.unstranded.bed.gz
│   │   ├── ASTARRseq_K562_KS91.hg38.Input.rep3.WGS.unstranded.bed.gz
│   │   ├── ASTARRseq_K562_KS91.hg38.Input.rep4.WGS.unstranded.bed.gz
│   │   ├── ASTARRseq_K562_KS91.hg38.Input.rep5.WGS.unstranded.bed.gz
│   │   ├── ASTARRseq_K562_KS91.hg38.Input.rep6.WGS.unstranded.bed.gz
│   │   ├── ASTARRseq_K562_KS91.hg38.Output.rep1.WGS.unstranded.bed.gz
│   │   ├── ASTARRseq_K562_KS91.hg38.Output.rep2.WGS.unstranded.bed.gz
│   │   ├── ASTARRseq_K562_KS91.hg38.Output.rep3.WGS.unstranded.bed.gz
│   │   └── ASTARRseq_K562_KS91.hg38.Output.rep4.WGS.unstranded.bed.gz
│   └── fragment
│
├── STARR_ATAC_K562_Reddy_KS274
│   ├── fragment_counts
│   └── fragment
│
├── STARR_ATAC_K562_Reddy_KSMerge
│   ├── fragment_counts
│   └── fragment
│
├── STARR_WHG_K562_Reddy_A001
│   ├── fragment_counts
│   │   ├── WSTARRseq_K562_A001.hg38.Input.rep1.WGS.unstranded.bed.gz
│   │   ├── WSTARRseq_K562_A001.hg38.Input.rep2.WGS.unstranded.bed.gz
│   │   ├── WSTARRseq_K562_A001.hg38.Input.rep3.WGS.unstranded.bed.gz
│   │   ├── WSTARRseq_K562_A001.hg38.Input.rep4.WGS.unstranded.bed.gz
│   │   ├── WSTARRseq_K562_A001.hg38.Output.rep1.WGS.unstranded.bed.gz
│   │   ├── WSTARRseq_K562_A001.hg38.Output.rep2.WGS.unstranded.bed.gz
│   │   └── WSTARRseq_K562_A001.hg38.Output.rep3.WGS.unstranded.bed.gz
│   └── fragment
│
├── MPRA_Tiling_K562_Tewhey_Hannah
│   ├── fragment_counts
│   │   ├── TMPRA_K562_OL13_20220512.hg19.raw. Input .rep[1-4].stranded_pos.bed
│   │   ├── TMPRA_K562_OL13_20220512.hg19.raw. Output.rep[1-4].stranded_pos.bed
│   │   ├── TMPRA_K562_OL13_20220512.hg19.norm.Input .rep[1-4].stranded_pos.bed
│   │   ├── TMPRA_K562_OL13_20220512.hg19.norm.Output.rep[1-4].stranded_pos.bed
│   │   │ 
│   │   ├── TMPRA_K562_OL13_20220512.hg19.norm.Input .mean.stranded_pos.bed
│   │   ├── TMPRA_K562_OL13_20220512.hg19.norm.Output.mean.stranded_pos.bed
│   │   ├── TMPRA_K562_OL13_20220512.hg19.norm.Log2FC.mean.stranded_pos.bed
│   │   │ 
│   │   ├── TMPRA_K562_OL43_20221003.hg38.raw. Input .rep[1-6].stranded_pos.bed
│   │   ├── TMPRA_K562_OL43_20221003.hg38.raw. Output.rep[1-5].stranded_pos.bed
│   │   ├── TMPRA_K562_OL43_20221003.hg38.norm.Input .rep[1-6].stranded_pos.bed
│   │   ├── TMPRA_K562_OL43_20221003.hg38.norm.Output.rep[1-5].stranded_pos.bed
│   │   │ 
│   │   ├── TMPRA_K562_OL43_20221003.hg38.norm.Input .mean.stranded_pos.bed
│   │   ├── TMPRA_K562_OL43_20221003.hg38.norm.Output.mean.stranded_pos.bed
│   │   ├── TMPRA_K562_OL43_20221003.hg38.norm.Log2FC.mean.stranded_pos.bed
│   │   │ 
│   │   ├── TMPRA_K562_OL45_20220927.hg38.raw. Input .rep[1-4].stranded_pos.bed
│   │   ├── TMPRA_K562_OL45_20220927.hg38.raw. Output.rep[1-4].stranded_pos.bed
│   │   ├── TMPRA_K562_OL45_20220927.hg38.norm.Input .rep[1-4].stranded_pos.bed
│   │   ├── TMPRA_K562_OL45_20220927.hg38.norm.Output.rep[1-4].stranded_pos.bed
│   │   │ 
│   │   ├── TMPRA_K562_OL45_20220927.hg38.norm.Input .mean.stranded_pos.bed
│   │   ├── TMPRA_K562_OL45_20220927.hg38.norm.Output.mean.stranded_pos.bed
│   │   ├── TMPRA_K562_OL45_20220927.hg38.norm.Log2FC.mean.stranded_pos.bed
│   │   │
│   │   └── summary
│   │       ├── TMPRA_K562_OL13_20220512.hg19.raw.stranded_pos.tsv 
│   │       ├── TMPRA_K562_OL13_20220512.hg19.norm.stranded_pos.tsv 
│   │       ├── TMPRA_K562_OL43_20221003.hg38.raw.stranded_pos.tsv 
│   │       ├── TMPRA_K562_OL43_20221003.hg38.norm.stranded_pos.tsv 
│   │       ├── TMPRA_K562_OL45_20220927.hg38.raw.stranded_pos.tsv 
│   │       └── TMPRA_K562_OL45_20220927.hg38.norm.stranded_pos.tsv 
│   └── fragment
│       ├── TMPRA_K562_OL13_20220512.hg19.raw.stranded_pos.bed.gz 
│       ├── TMPRA_K562_OL43_20221003.hg38.raw.stranded_pos.bed.gz 
│       └── TMPRA_K562_OL45_20220927.hg38.raw.stranded_pos.bed.gz 
│
├── MPRA_Lenti_K562_Nadav_Vikram
│   ├── fragment_counts
│   |   ├── LMPRA_K562.hg38.Log2FC.unstranded.bed.gz
│   |   ├── LMPRA_K562.hg38.ZScore.unstranded.bed.gz
│   |   └── summary
│   │       ├── 
│   │       └── 
│   └── fragment
│
├── CRISPRi_FlowFISH_K562_Riley_JinWoo
│   └── guide_scores
│       ├── CRISPRi_HCRFF_K562.hg38.ZScore.unstranded.bed.gz
│       ├── CAPRIN1_HCRFF_rAVG.log2FC_2.bed
│       ├── CAT_HCRFF_rAVG.log2FC_2.bed
│       ├── CD164_HCRFF_rAVG.log2FC_2.bed
│       ├── ERP29_HCRFF_rAVG.log2FC_2.bed
│       ├── FADS1_HCRFF_rAVG.log2FC_2.bed
│       ├── FADS2_HCRFF_rAVG.log2FC_2.bed
│       ├── FADS3_HCRFF_rAVG.log2FC_2.bed
│       ├── FEN1_HCRFF_rAVG.log2FC_2.bed
│       ├── GATA1_HCRFF_rAVG.log2FC_2.bed
│       ├── HBE1_HCRFF_rAVG.log2FC_2.bed
│       ├── HBG1_HCRFF_rAVG.log2FC_2.bed
│       ├── HBG2_HCRFF_rAVG.log2FC_2.bed
│       ├── HBS1L_HCRFF_rAVG.log2FC_2.bed
│       ├── HDAC6_HCRFF_rAVG.log2FC_2.bed
│       ├── LMO2_HCRFF_rAVG.log2FC_2.bed
│       ├── MEF2C_HCRFF_rAVG.log2FC_2.bed
│       ├── MYB_HCRFF_rAVG.log2FC_2.bed
│       ├── MYC_HCRFF_rAVG.log2FC_2.bed
│       ├── NMU_HCRFF_rAVG.log2FC_2.bed
│       ├── PVT1_HCRFF_rAVG.log2FC_2.bed
│       └── summary
│           ├── track_info.tsv
│           ├── metadata.tsv
│           └── metadata.library_design.tsv
│
└── CRISPRi_Growth_K562_Gersbach_JinWoo
    └── guide_scores
        ├── CRISPRi_rAVG_log2FC_2.wig
        ├── CRISPRi_rAVG_log2FC_2.bed
        ├── CRISPRi_Growth_K562.hg38.ZScore.unstranded.bed.gz
        └── summary
            ├── track_info.tsv
            └── metadata.tsv

HiC assay

Summary

PROJECT/results/assay_hic
├── hic_insitu_K562_ENCSR545YBD
├── hic_intact_K562_ENCSR479XDG
└── hic_intact_K562_deep