Nextflow pipeline for processing of GPSeq data

Genomic loci positioning by sequencing (GPSeq): genome-wide method for inferring distances to the nuclear lamina all along the nuclear radius.

Getting Started

The whole pipeline can be cloned in your current working directory with:

git clone https://github.com/BiCroLab/nextflow-gpseq
cd nextflow-gpseq

Requirements

conda create -n nextflow -c conda-forge -c bioconda nextflow=23.10.0 singularity=3.8*

• nextflow (tested onversion 23.10 or higher)
• singularity (tested on version 3.8.6)

To test the pipeline with default settings and a test dataset: nextflow run main.nf -profile test

Running the pipeline with your own dataset

1. Make a samplesheet.csv containing the following columns: sample,fastq,barcode,condition.
   The file should be comma separated and sorted by digestion time-point in seconds.

2. Check and adjust required settings in nextflow.config and igenomes.config.

3. Run the pipeline with the following command:
   

   nextflow run main.nf --samplesheet /path/to/samplesheet.csv --outdir /path/to/results --fasta /path/to/reference.fa --bwt2index /path/to/bowtie2/index/folder -resume
   

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General Settings:

Setting	Description
enzyme / cutsite	enzyme name (e.g. DpnII) and recognition motif (e.g. GATC)
binsizes	list of comma-separated binsizes for calculating GPSeq scores; formula: window:smoothing: "1e+05:1e+05,1e+05:1e+04,5e+04:5e+04"
normalization	data normalization by library / chromosome ("lib" / "chrom") "lib": each experiment is normalized based on its total read count "chrom": normalization is applied independently for each chromosome
site_domain	param affecting which restriction sites are considered for computing score default value is "universe"; also see: "separate"/"union" for a detailed explanation about all existing site_domain settings, please refer to the supplementary information of our GPSeq paper.
score_outlier_tag	setting to filter out outliers (default: "iqr:1.5")
bed_outlier_tag	setting to filter out outliers (default: "chisq:0.01")

Genome Settings:

Genome-related settings can be modified from igenomes.config:

Setting	Description
fasta	path to reference genome.fa genome sequence
fasta_index	path to corresponding genome.fa.fai genome index
bowtie2	path to directory containing bowtie2 index
mask_bed	path to bed file containing regions to be masked

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Outputs