brickmanlab/primeseq is a bioinformatics preprocessing pipeline for PRIME-seq datasets.

1. Read QC (FastQC)
2. Align reads using (StarSolo)
3. Merge well sheet with according barcodes
4. Present QC for raw reads (MultiQC)

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

sample,fastq_1,fastq_2,plate_id
CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,1

wells.csv

pool,well,sample
CONTROL_REP1,A1,Sample_1

Each row represents paired end FASTQ reads.

Now, you can run the pipeline using:

nextflow run brickmanlab/primeseq \
    -with-tower \
    -profile ku_sund_danhead,dancmpn02fl \
    --genome GRCm39-2024-A \
    --input samplesheet.csv \
    --wells wells.csv \
    --outdir output

or by creating slurm batch script (align.sbatch)

#!/bin/bash

#SBATCH --job-name=align
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=NONE
#SBATCH -c 1
#SBATCH --mem=2gb
#SBATCH --time=1-00:00:00
#SBATCH --output=align.log
#SBATCH -w dancmpn02fl

module load openjdk/20.0.0 nextflow/23.04.1.5866 singularity/3.8.0

nextflow run /home/fdb589/primeseq \
    -with-tower \
    -profile ku_sund_danhead,dancmpn02fl \
    --genome GRCm39-2024-A \
    --input samplesheet.csv \
    --wells wells.csv \
    --outdir results

brickmanlab/primeseq was originally introduced by Nazmus Salehin and written by Martin Proks.

If you would like to contribute to this pipeline, please see the contributing guidelines.

If you use brickmanlab/primeseq for your analysis, please cite it using the following doi: 10.5281/zenodo.13167325

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.