README.md

(S)ingle (E)nd (A)ntibody (SEQ)uencing pipeline

DX-CWL COMPATIBLE

Chromatin Single-End analysis pipeline

The SEASEQ Pipeline is a complete analysis pipeline for CHiP sequencing single-end data.

The analysis pipeline includes mapping using bowtie, peak-calls using MACS and SICER, motif analysis using meme suite, enhancers & super-enhancers using ROSE, bam density plots using BAM2GFF.

INSTRUCTIONS

To run SEASEQ pipeline, you will need Linux, or some compatible container technology, CWL (Common Workflow Language), and about 30GB of supplemental data.

PROGRAMS & VERSIONS

Programs and versions used to build and test the pipeline.

• bowtie v. 1.2.2
• fastqc v. 0.11.5
• samtools v. 1.9
• R v. 3.6.1
• macs v. 041014
• SICER2 v. 1.0.2
• meme v. 4.11.2
• spp v. 1.16.0
• bedtools/2.25.0
• python v. 3.7.0
• java v. 1.8.0_60
• perl v. 5.10.1
• wigToBigWig v. 4
• bedops v. 2.4.2
• igvtools v. 2.3.2
• ROSE v. 1.1.0
• BAM2GFF v. 1.1.0

REQUIREMENT

• INPUT

inputyml.yml file

Example of an inputyml.yml file.

reference: 
  class: Directory
  location: /path/to/genome_reference+index

fastqfile: 
  class: File
  path: /path/to/fastqfile

keep_dup: all

chromsizes: 
  class: File
  path: /path/to/chromsizes_file

blacklistfile:
  class: File
  path: /path/to/blacklist_file

gtffile:
  class: File
  path: /path/to/gtf_file

motifdatabases:
  - { class: File, path: /path/to/meme_motif1 }
  - { class: File, path: /path/to/meme_motif2 }

• OUTPUTS

All outputfiles will be saved in current working directory

EXAMPLE SYNTAX using CWLTOOL

cwltool /path/to/folder/cwl/seaseq_pipeline.cwl inputyml.yml