README.md

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

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

• bowtie v. 1.2.2
• fastqc v. 0.11.5
• samtools v. 1.9
• R v. 3.6.1
• macs v. 041014
• SICER2 v. 1.0.1
• meme v. 4.11.2
• phantompeakqualtools v. 1.2.1.1
• 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

REQUIREMENTS

INPUT YML

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

fastqfile: 
  - { class: File, path: /path/to/fastqfile1 }
  - { class: File, path: /path/to/fastqfile2 }

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 }

EXAMPLE

We provided example instructions for running under Toil on our St. Jude HPC LSF cluster.