List of steps in the analyses

Data preparation

This part is mainly about

  • Downloading data to PROJECT/data folder
  • Preparing data from PROJECT/data to PROJECT/results folder
  • Generating metadata for down stream analysis

Step: Preparing FCC data

Title Subtitle
Prepare ENCODE ATAC/DNase Peaks 01 Generate download script to download the data
Prepare ENCODE ATAC/DNase Peaks 02 Download the data
Prepare ENCODE ATAC/DNase Peaks 03 Prepare the data
Prepare ENCODE ATAC/DNase Peaks 04 Generate metadata for the peak file
Prepare Lenti-MPRA data 01 Get K562 MPRA data files from Nadav lab
Prepare Lenti-MPRA data 02 Explore Lenti-MPRA data files
Prepare Lenti-MPRA data 03 Export Lenti-MPRA data file from PROJECT/data to PROJECT/results folder
Prepare STARR-seq data 01 Get K562 STARR-seq data files from Reddy lab
Prepare STARR-seq data 02 Explore STARR-seq data files
Prepare STARR-seq data 031 Prepare STARR-seq data files from PROJECT/data to PROJECT/results folder
Prepare STARR-seq data 032 Prepare ATAC-STARR KS274 files from PROJECT/data to PROJECT/results folder
Prepare STARR-seq data 04 Create metadata for STARR-seq data files
Prepare Tiling MPRA data 01 Get K562 MPRA data files from Tewhey lab
Prepare Tiling MPRA data 02 Explore Tiling MPRA data files
Prepare Tiling MPRA data 03 Extract fragment counts from Tiling MPRA data
Prepare Tiling MPRA data 04 Covert count matrix to bed format
Prepare Tiling MPRA data 05 Liftover OL13 fragments from hg19 to hg38
Prepare Tiling MPRA data 06 Get the genomic range of fragments designed in TMPRA
Prepare Tiling MPRA data 07 Create metadata for Tiling MPRA data files
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Step: Preparing Hi-C data

Title Subtitle
Prepare Hi-C data 01 (in situ Hi-C) Generate download script to download the data
Prepare Hi-C data 01 (intact Hi-C) Generate download script to download the data
Prepare Hi-C data 01 (intact Hi-C; deep) Download data
Prepare Hi-C data 02 (in situ Hi-C) Download the data
Prepare Hi-C data 02 (intact Hi-C) Download the data
Prepare Hi-C data 02 (intact Hi-C; deep) Check downloaded data
Prepare Hi-C data 03 (in situ Hi-C) Check downloaded data
Prepare Hi-C data 03 (intact Hi-C) Check downloaded data
Prepare Hi-C data 11 (in situ Hi-C) Prepare data (Loop)
Prepare Hi-C data 11 (intact Hi-C) Prepare data (Loop)
Prepare Hi-C data 11 (intact Hi-C; deep) Prepare data (Loop)
Prepare Hi-C data 12 (in situ Hi-C) Prepare data (TAD)
Prepare Hi-C data 12 (intact Hi-C) Prepare data (TAD)
Prepare Hi-C data 12 (intact Hi-C; deep) Create metadata
Prepare Hi-C data 13 (in situ Hi-C) Create metadata
Prepare Hi-C data 13 (intact Hi-C) Create metadata
Prepare Hi-C data 21 (in situ Hi-C) Explore data (Loop)
Prepare Hi-C data 21 (intact Hi-C) Explore data (Loop)
Prepare Hi-C data 21 (intact Hi-C; deep) Explore data (Loop)
Prepare Hi-C data 22 (in situ Hi-C) Explore data (TAD)
Prepare Hi-C data 22 (intact Hi-C) Explore data (TAD)
Prepare Hi-C data 22 (intact Hi-C; deep) Explore data (Matrix)
Prepare Hi-C data 23 (in situ Hi-C) Explore data (Matrix)
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Step: Preparing ChIP-seq data

Title Subtitle
Prepare ENCODE ChIP-seq Histone 01 Generate download script to download the data
Prepare ENCODE ChIP-seq Histone 02 Download the data
Prepare ENCODE ChIP-seq Histone 03 Check download files
Prepare ENCODE ChIP-seq Histone 11 Export region data to result folder
Prepare ENCODE ChIP-seq Histone 11 Export region data to result folder
Prepare ENCODE ChIP-seq Histone 12 Export signal data to result folder
Prepare ENCODE ChIP-seq Histone 12 Export signal data to result folder
Prepare ENCODE ChIP-seq Histone 13 Create metadata table of region
Prepare ENCODE ChIP-seq Histone 13 Create metadata table of region
Prepare ENCODE ChIP-seq Histone 14 Create metadata table of signal
Prepare ENCODE ChIP-seq Histone 14 Create metadata table of signal
Prepare ENCODE ChIP-seq Subset 01 Generate download script to download the data
Prepare ENCODE ChIP-seq Subset 02 Download the data
Prepare ENCODE ChIP-seq Subset 03 Sort data and export to result folder
Prepare ENCODE ChIP-seq Subset 04 Create metadata table for downstream analysis
Prepare ENCODE ChIP-seq TF 01 Generate download script to download the data
Prepare ENCODE ChIP-seq TF 02 Download the data (Region)
Prepare ENCODE ChIP-seq TF 02 Download the data (Signal fold change)
Prepare ENCODE ChIP-seq TF 03 Check download files
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Step: Preparing Annotations

Title Subtitle
Prepare ENCODE RNA-seq 01 Generate download script to download the data
Prepare ENCODE RNA-seq 02 Download the data
Prepare ENCODE RNA-seq 03 Explore and visualize the data
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Step: Preparing Regions

Title Subtitle
Prepare ASTARR CSAW Peaks 01 Acquire data
Prepare ASTARR CSAW Peaks 02 Prepare data
Prepare ASTARR CSAW Peaks 03 Create metadata
Prepare ASTARR CSAW Peaks 03 Explore the data
Prepare ASTARR Input MACS Peaks (Merged) 01 Prepare K562 accessible regions
Prepare ASTARR Input MACS Peaks (Merged) 02 Create metadata table for downstream analysis
Prepare ASTARR Input MACS Peaks (Merged) 03 Explore and visualize the data
Prepare ASTARR Input MACS Peaks (Replicates) 01 Prepare K562 accessible regions
Prepare ASTARR Input MACS Peaks (Replicates) 02 Create metadata
Prepare ASTARR Input MACS Peaks (Replicates) 03 Explore and visualize the data
Prepare CRISPRi Growth data 01 Prepare data
Prepare CRISPRi Growth data 02 Generate metadata of the peak file
Prepare CRISPRi Growth data 03 Explore and visualize the data
Prepare CRISPRi HCRFF data 01 Generate download script to download the data
Prepare CRISPRi HCRFF data 02 Download the data
Prepare CRISPRi HCRFF data 03 Prepare the data
Prepare CRISPRi HCRFF data 04 Generate metadata for the peak file
Prepare CRISPRi HCRFF data 05 Explore and visualize the data
Prepare ENCODE ATAC/DNase Peaks 01 Generate download script to download the data
Prepare ENCODE ATAC/DNase Peaks 02 Download the data
Prepare ENCODE ATAC/DNase Peaks 03 Prepare the data
Prepare ENCODE ATAC/DNase Peaks 04 Generate metadata for the peak file
Prepare ENCODE ATAC/DNase Peaks 05 Explore and visualize the data
Prepare ENCODE ATAC/DNase Peaks 06 Comparison-region counts
Prepare ENCODE ATAC/DNase Peaks 06 Comparison-genomic distribution
Prepare ENCODE Chromatin State 01 Generate download script to download the data
Prepare ENCODE Chromatin State 02 Download the data
Prepare ENCODE Chromatin State 03 Prepare region files
Prepare ENCODE Chromatin State 04 Create metadata table for downstream analysis
Prepare ENCODE Chromatin State 05 Explore and visualize the data
Prepare ENCODE E2G data 01 Arrange region data
Prepare ENCODE E2G data 02 Create metadata table
Prepare ENCODE E2G data 03 Explore and summarize data
Prepare Junke peak call region 01 View files
Prepare Junke peak call region 02 Decompress files
Prepare Junke peak call region 03 Prepare data
Prepare Junke peak call region 04 Generate metadata of the peak file
Prepare Junke peak call region 05 Explore and visualize the data
Prepare TF Modules 01 Export the data
Prepare TF Modules 02 Create metadata table for downstream analysis
Prepare TF Modules 03 Explore and visualize the data
Prepare TSS annotation 01 Prepare K562 TSS annotation
Prepare TSS annotation 02 Create metadata table for downstream analysis
Prepare TSS annotation 03 Explore and visualize the data
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Region coverage and annotation

Step: Region summary

Title Subtitle
Calculate GC% of ATAC regions 01 Run bedtools nuc
Calculate GC% of ATAC regions 01 Run bedtools nuc
Calculate GC% of ATAC regions 01 Run bedtools nuc
Prepare TF Modules 01 Explore the data
Prepare TF Modules 01 Explore the data
Region annotation 11 (ASTARR MACS peaks) Summarize annotations (Main)
Region annotation 11 (ASTARR MACS peaks) Summarize annotations (Main)
Region annotation 11 (ASTARR MACS peaks) Summarize annotations (Main)
Region annotation 11 (ASTARR MACS peaks) Summarize annotations (Main)
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Step: Region coverage (FCC)

Step: Region coverage (ChIP-seq)

Step: Region annotation

Title Subtitle
Annotation of ATAC (ASTARR Input) 01 Intersection (Main)
Annotation of ATAC (ASTARR Input) 02 Intersection (Hi-C)
Annotation of ATAC (ASTARR Input) 03 Intersection (ChIP-seq Subset)
Annotation of ATAC (ASTARR Input) 04 Intersection (ChIP-seq Histone)
Annotation of ATAC (ASTARR Input) 05 Intersection (ChIP-seq TF Full)
Annotation of ATAC (ASTARR Input) 11 Arrange region pairs (Main)
Annotation of ATAC (ASTARR Input) 21 01 Summarize ATAC w/ STARR/MRPA peaks
Annotation of ATAC (ASTARR Input) 21 02 Summarize ATAC w/ CRISPRi-HCR FlowFISH CASA peaks
Annotation of ATAC (ASTARR Input) 21 03 Summarize ATAC w/ CRISPRi-Growth significant DHS
Annotation of ATAC (ASTARR Input) 21 04 Summarize ATAC w/ TSS
Annotation of ATAC (ASTARR Input) 21 05 Summarize ATAC w/ ENCODE E2G links
Annotation of ATAC (ASTARR Input) 21 06 Summarize ATAC w/ ENCODE chromatin states
Annotation of ATAC (ASTARR Input) 21 07 Summarize ATAC w/ previous studied CREs
Annotation of ATAC (ASTARR Input) 21 06 Explore/Visualize ATAC w/ ENCODE chromatin states
Annotation of ATAC (ASTARR Input) 22 01 Explore/Visualize ATAC w/ STARR/MRPA peaks
Annotation of ATAC (ASTARR Input) 22 02 Explore/Visualize ATAC w/ CRISPRi-HCR FlowFISH CASA peaks
Annotation of ATAC (ASTARR Input) 22 03 Explore/Visualize ATAC w/ CRISPRi-Growth significant DHS
Annotation of ATAC (ASTARR Input) 22 04 Explore/Visualize ATAC w/ TSS
Annotation of ATAC (ASTARR Input) 22 05 Explore/Visualize ATAC w/ ENCODE E2G links
Annotation of ATAC (ASTARR Input) 31 Summarize regions with E2G regulated links
Annotation of ATAC (ASTARR Input) 32 Summarize scores with E2G regulated links
Annotation of ATAC (ASTARR Input) 33 Explore/Visualize regions with E2G regulated links
Annotation of ATAC (ASTARR Input) 34 Explore/Visualize scores with E2G regulated links
Annotation of ATAC (ASTARR Input) 41 Summarize assay direction from STARR/MPRA
Annotation of ATAC (ASTARR Input) 42 Summarize assay votes from STARR/MPRA by directions
Annotation of ATAC (ASTARR Input) 42 Summarize assay votes from STARR/MPRA by directions (remove AR)
Annotation of ATAC (ASTARR Input) 43 Define proximal/distal-active/repressive CREs
Annotation of ATAC (ASTARR Input) 44 Explore/Visualize distribution of GC content and length
Annotation of ATAC (ASTARR Input) 45 Explore/Visualize STARR/MPRA CRE counts by assay direction
Annotation of ATAC (ASTARR Input) 46 Explore/Visualize STARR/MPRA CRE counts by assay
Annotation of ATAC (ASTARR Input) 47 Explore/Visualize STARR/MPRA CRE overlapped
Annotation of ATAC (ASTARR Input) 51 Concatenate ATAC with significant peaks of STARR/MPRA/CRISPR
Annotation of ATAC (ASTARR Input) 52 Summarize assay votes of STARR/MPRA/CRISPR
Annotation of ATAC (ASTARR Input) 53 Explore/Visualize STARR/MPRA/CRISPR CRE counts by assays
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This part is mainly about

  • FCC union peak set of cis-regulatory elements
  • Enrichment analysis of chromtain states and TFs
  • Quantitative comparison across assays

Testing

Below is a test notebook

Title Subtitle
Test ipynb for documentation Notebook with kernel R
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