README guideline

TEMPLATE README.md file (DELETE WHEN COMPLETED)

This is a template README file for pipelines that are already developed or under development. The aim of a README file is to provide the user with a guideline on how to use the pipeline, as well as to help the developer document their work.

Tips

• To include general links: [text for link](link).
• To include links to other pages of the repository: [text for link](page-repository/other-file)
• To make bullet points: * text or - text.
• To write in bold: **text**.
• To write in italics: _ text _.
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• Save README file as .md

< Pipeline title >

Pipeline overview

<Include a brief description of:

• the purpose of the pipeline.
• the type of data the pipeline analyses/processes.
• if the pipeline is related to a project(s). >

{e.g. (DELETE WHEN COMPLETED)

Assay for Ttransposase-Accessible Chromatin using sequencing (ATAC-seq) is a method to investigate the accessibility of choromatin and thus to determine regulatory mechanisms of gene expression. It can help to identify promoter regions and potential enhancers and silencers. ATAC-Seq has become popular for identifying accessible regions of the genome as it’s easier, faster and requires less cells than alternative techniques.

We have develop a pipeline that process and analyses ATAC-seq data, including pre-processing of samples, alignment, quality control, calling peaks and differential accessibility analysis. The steps to run this pipeline are detailed below. }

Requisites of the pipeline

<Include:

• Specify directory to submit the scripts from.
• Location of the config file required.
• Location of the project/data folder: raw data and output.
• Any required modules, software or tools, and their corresponding version if necessary. >

{e.g (DELETE WHEN COMPLETED)

• All steps should be run from the scripts directory.
• Users require a username folder in the ATACSeq/logFiles directory.
• The name of the project folder must be specified as the first argument on the command line (project name).
• Requires two config files in the ATACSeq/config directory:
  • config.txt with variables for bash scripts.
  • config.r with parameters for R scripts.
• Required modules:
  • samtools
  • macs v2
  • BEDtools }

Steps

<Step 1>

< Include:

• Brief description of what is done during this step.
• Each script that is run with a brief description of what it does and their location.
• Basic Command line to execute the script.
• Specify the parameters each script takes and whether they are optional (specified as [parameter]) or not (specified as (parameter)).
• If optional paremeters, list all the options and their description. >

{e.g. (DELETE WHEN COMPLETED)

1. Pre-analysis

sbatch --array="number of batch jobs" ATACSeq/jobSubmission/1_batchRunAlignment.sh (project name) [STEPS]

Performs pre-analysis of ATAC-seq data, including pre-alignment quality control, alignment and post-alignment quality control of samples.

-scripts executed-

• preScripts/fastqc.sh : FastQC for pre-alignment quality control.
• preScripts/fastp.sh : FastP for trimming samples.
• ATACSeq/preprocessing/alignment.sh : Alingment of samples to reference genome using Bowtie2.
• ATACSeq/preprocessing/calcENCODEQCMetrics.sh : ENCODE QC metrics are calculated on aligned samples.

-parameters-

• --array: number of batch jobs, each number matches a sample.
• (project-name) the name of the project folder in the main data type data directory. -optional-
• [STEPS] Option to combine steps with desired steps included as single string, i.e. FASTQC,TRIM. Default if left blank is to run all steps. Options:
  • FASTQC: Perform only quality control. Run only fastqc.sh on samples.
  • TRIM: Perform only trimming on samples. Run only fastp.sh on samples.
  • ALIGN: Align samples. Run only alignment.sh on samples.
  • ENCODE: Calculation of ENCODE QC metrics.

-outputs-

• FASTQC: FastQC results (includes reports) in /1_raw/fastqc
• TRIM: FastP results (includes trimmed.fastq.gz reads and reports) in /2_trimmed
• ALIGN: Aligned reads in /3_aligned
  • dupMetrics.txt : duplicates report
  • .filt.nodup.bam : filtered, no duplicated aligned reads
  • .filt.nodup.bam.bai : index final bam file
• ENCODE : ENCODE QC metrics results in /3_aligned/ENCODEMetrics
  • .flagstat.qc
  • .pbc.qc }

<Step 2>

<Step 3>

<Step ...>

How to contribute (Optional)

< Include how to contribute to the development of the pipeline or point to where users can find more information about how to raise an issue or enhancement suggestion.>

Contributors (Optional)

< Include who contributes to the development of the pipeline. Include contact details if desired.>

Publications (Optional)

<Include related publications to the project/pipeline.>

References/Resources (Optional)

<Include references used to build the pipeline, useful resources or guidance used.>

{e.g. (DELETE WHEN COMPLETED)

The development of this pipeline has been largely based on the approach described in: Yan, F., Powell, D.R., Curtis, D.J. et al. From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis. Genome Biol 21, 22 (2020). https://doi.org/10.1186/s13059-020-1929-3

}