12 Results (FCC)

Results: FCC Assays — Fragment Properties

PROJECT/results/assay_fcc
└── <STARR>
    └── fragment_nuc

Results: FCC Assays — Fragment Coverage and library size

PROJECT/results/assay_fcc/<STARR/MPRA>
└── fragment_counts
    └── summary
        ├── metadata.tsv
        ├── metadata.size.tsv
        ├── result.size.{0..N}.csv
        ├── result.size.concat.csv
        └── 

Results: FCC Assays — Fragment Coverage and bigwig tracks

Results: FCC Assays — Region Coverage and STARR-seq library complexity

• overlap_fragment
  • intersection between region and fragment
• overlap_fragment_unique
  • unique fragments from the region-fragment intersection
• overlap_fragment_one2one
  • for all regions intersected with each fragment, pick the region-fragment pair with the longest overlap
• overlap_count_one2one
  • count total fragments for each region
• overlap_count_one2one_unique
  • count unique fragments for each region
• overlap_count
  • count total fragments for each region

PROJECT/results/assay_fcc/<STARR>/coverage/<Region Folder>/<Region Label>
├── overlap_fragment
|   └── summary
├── overlap_fragment_unique
|   └── summary
|       ├── result.size.{1..N}.csv
|       ├── result.size.concat.csv
|       └── result.size.summary.tsv
├── overlap_fragment_one2one
|   └── summary
|       ├── result.size.{1..N}.csv
|       ├── result.size.csv
|
├── overlap_count
|   └── summary
└── overlap_count_unique
    └── summary

PROJECT/results/assay_fcc/<STARR/TMPRA>
└── coverage
    └── <Region Folder>
        └── <Region Label>
            ├── overlap_fragment
            |   └── summary
            |
            ├── overlap_fragment_unique //
            |   └── summary
            |       ├── result.size.{0..N}.tsv
            |       ├── result.size.concat.tsv
            |       └── 
            |
            ├── overlap_fragment_one2one //
            |   └── summary
            |       ├── result.size.{0..N}.tsv
            |       ├── result.size.concat.tsv
            |       └── 
            |
            ├── overlap_count/score
            |   └── summary
            |       ├── data_list_count_column.rds
            |       ├── data_list_score.rds         // matrices: raw, cpm, rpkm, tpm, deseq, edger (TMM)
            |       ├── data_edger.rds
            |       ├── data_deseq.rds
            |       ├── result.Log2FC.deseq.tsv
            |       ├── result.Log2FC.edger.tsv
            |       ├── result.score.mean.tsv       // mean of rpkm, tpm
            |       └── 
            |
            ├── overlap_count_unique
            
            

Results: FCC Assays — Region Coverage and DESeq2/EdgeR

overlap_count
└── summary
    ├── data_list_count_column.rds
    ├── data_list_score.rds         // matrices: raw, cpm, rpkm, tpm, deseq, edger (TMM)
    ├── data_edger.rds
    ├── data_deseq.rds
    ├── result.Log2FC.deseq.tsv
    ├── result.Log2FC.edger.tsv
    ├── result.score.mean.tsv       // mean of rpkm, tpm
    └── 

Results: FCC Assays (Detailed)

Folder

PROJECT/results/assay_fcc
├── <STARR>
|   ├── fragment
|   ├── fragment_nuc
|   ├── fragment_counts
|   |   └── summary
|   └── coverage
|       ├── track
|       └── <Region Folder>
|           └── <Region Label>
|               ├── overlap_fragment
|               ├── overlap_fragment_unique
|               ├── overlap_fragment_one2one
|               ├── overlap_count
|               └── overlap_count_unique
|
├── <TMPRA>
|   ├── fragment
|   ├── fragment_nuc
|   ├── fragment_counts
|   └── coverage
|       ├── track
|       └── <Region Folder>
|           └── <Region Label>
|               ├── overlap_fragment
|               └── overlap_count
|
├── <LMPRA>
|   ├── fragment
|   ├── fragment_nuc
|   ├── fragment_counts
|   └── coverage
|       ├── track
|       └── <Region Folder>
|           └── <Region Label>
|               ├── overlap_fragment
|               └── overlap_score
|
└── <CRISPRi>
    ├── guide_scores
    CRISPRi_HCRFF_K562.hg38.ZScore.unstranded.bed.gz
    CRISPRi_HCRFF_K562.hg38.ZScore.filtered.unstranded.bed.gz
    |   └── summary
    |       ├── track_info.tsv
    |       └── metadata.tsv
    ├── guide_scores_filter
    |   └── summary
    |       └── metadata.tsv
    └── coverage
        └── <Region Folder>
            └── <Region Label>
                ├── overlap_guide
                └── overlap_score

Files

PROJECT/results/assay_fcc
├── CRISPRi_FlowFISH_K562_Riley_JinWoo
│   └── guide_scores
│       ├── CRISPRi_HCRFF_K562.hg38.ZScore.unstranded.bed.gz
│       ├── CRISPRi_HCRFF_K562.hg38.ZScore.filtered.unstranded.bed.gz

PROJECT/results/region_annotation