Quickstart + Usage

After installing Consenrich, you can run it via the command line (consenrich -h) or programmatically using the Python/Cython consenrich.core.

Getting Started: Minimal Example

A brief analysis using H3K27ac (narrow) ChIP-seq data generated from human tissue samples is carried out for demonstration.

Input Data

The input data in this example consists of four donors’ treatment and control samples (epidermal tissue) from ENCODE.

Input Data

Experiment	Biosample	H3K27ac Alignment	Control Alignment
ENCSR214UZE	Epidermis/Female/71	ENCFF793ZHL.bam	ENCFF444WVG.bam
ENCSR334DRN	Epidermis/Male/67	ENCFF647VPO.bam	ENCFF619NYP.bam
ENCSR340ZTB	Epidermis/Female/80	ENCFF809VKT.bam	ENCFF898LKJ.bam
ENCSR386CKJ	Epidermis/Male/75	ENCFF295EFL.bam	ENCFF490MWV.bam

Download Alignment Files from ENCODE

Copy+paste the following to your terminal to download and index the BAM files for this demo.

You can also use curl -O <URL> in place of wget <URL> if the latter is not available on your system.

encodeFiles=https://www.encodeproject.org/files
for file in ENCFF793ZHL ENCFF647VPO ENCFF809VKT ENCFF295EFL; do
    wget "$encodeFiles/$file/@@download/$file.bam"
done
for ctrl in ENCFF444WVG ENCFF619NYP ENCFF898LKJ ENCFF490MWV; do
    wget "$encodeFiles/$ctrl/@@download/$ctrl.bam"
done
samtools index -M *.bam

Using a YAML Configuration file

Tip

Refer to the <process,observation,etc.>Params classes in module in the consenrich.core for complete documentation of configuration options.

Copy and paste the following YAML into a file named demoHistoneChIPSeq.yaml:

experimentName: demoHistoneChIPSeq

genomeParams:
  name: hg38
  chromosomes: [chr21, chr22] # remove this line to run genome-wide
  excludeForNorm: [chrX, chrY]

inputParams:
  bamFiles:
    - ENCFF793ZHL.bam
    - ENCFF647VPO.bam
    - ENCFF809VKT.bam
    - ENCFF295EFL.bam
  bamFilesControl:
    - ENCFF444WVG.bam
    - ENCFF619NYP.bam
    - ENCFF898LKJ.bam
    - ENCFF490MWV.bam

Control Inputs

You can omit inputParams.bamFilesControl for ATAC-seq, DNase-seq, Cut&Run, and other assays where no input control is available or applicable.

Run Consenrich

% consenrich --config demoHistoneChIPSeq.yaml --verbose

Results

• We display Consenrich results (blue) over a 250 kb locus in human chromosome 22