Chienlab-RNAseq

Introduction

chienlab-rnaseq is a Nextflow pipeline for performing bacterial RNA-Seq analysis.

This pipeline has been heavily inspired by the BactSeq pipeline.

Pipeline summary

The pipeline will perform the following steps:

1. Trim adaptors from reads, performs QC, and filters reads (Fastp)
2. Align reads to reference genome (BWA-MEM)
3. Performs read quantificantion (Rsubread)
4. Generates BigWig files for visualization in genome browsers (deeptools)
5. Size-factor scaling and gene length (RPKM) scaling of counts (TMM from edgeR)
6. Principal component analysis (PCA) of normalised expression values
7. Differential gene expression (DESeq2) (optional)

Installation

You will need to install Nextflow (version 21.10.3+).

Usage:
nextflow run baldikacti/chienlab-rnaseq --data_dir [dir] --sample_file [file] --ref_genome [file] --ref_ann [file] -profile conda [other_options]

Mandatory arguments:
  --data_dir [file]               Path to directory containing FastQ files.
  --ref_genome [file]             Path to FASTA file containing reference genome sequence (bwa) or multi-FASTA file containing coding gene sequences (kallisto).
  --ref_ann [file]                Path to GFF file containing reference genome annotation.
  --sample_file [file]            Path to file containing sample information.
  -profile [str]                  Configuration profile to use.
                                  Available: conda

Other options:
  --cont_tabl [file]              Path to tsv file containing contrasts to be performed for differential expression.
  --l2fc_thresh [str]             Absolute log2(FoldChange) threshold for identifying differentially expressed genes. Default = 1.
  --outdir [file]                 The output directory where the results will be saved (Default: './results').
  --p_thresh [str]                Adjusted p-value threshold for identifying differentially expressed genes. Default = 0.05.
  --max_memory ['32.GB']          Maximum available memory in the system
  --max_cpus [int]                Maximum available cpu's in the system
  --max_time ['10.h']             Maximum time requested time for the pipeline
  -name [str]                     Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic.

Explanation of parameters:

• ref_genome: genome sequence for mapping reads.
• ref_ann: annotation of genes/features in the reference genome.
• sample_file: TSV file containing sample information (see below)
• data_dir: path to directory containing FASTQ files.
• cont_tabl: (optional) table of contrasts to be performed for differential expression.
• p_thresh: adjusted p-value threshold for identifying differentially expressed genes. Default = 0.05.
• l2fc_thresh: absolute log2(FoldChange) threshold for identifying differentially expressed genes. Default = 1.
• outdir: the output directory where the results will be saved (Default: ./results).
• -resume: will re-start the pipeline if it has been previously run.

Required input

• Genome sequence: FASTA file containing the genome sequence. Can be retrieved from NCBI.

• Gene annotation file: GFF file containing the genome annotation. Can be retrieved from NCBI.

• Sample file: TSV file containing sample information. Must contain the following columns:

  • sample: sample ID
  • file1: name of the first FASTQ file.
  • file2: name of the second FASTQ file. (For single-end sequences, leave blank)
  • group: grouping factor for differential expression and exploratory plots.
  • rep_no: repeat number (if more than one sample per group).
  • paired: data are paired-end? (0 = single-end, 1 = paired-end).
  • strandedness : Is data stranded? Options: unstranded, forward, reverse.

  Example:

  If data are single-end, leave the file2 column blank.

  Sample file can contain a mix of single-end and paired-end, and a mix of stranded and unstranded samples.

reference.tsv

sample	file1	file2	group	rep_no	paired	strandedness
AS_1	SRX1607051_T1.fastq.gz		Artificial_Sputum	1	0	reverse
AS_2	SRX1607052_T1.fastq.gz		Artificial_Sputum	2	0	reverse
AS_3	SRX1607053_T1.fastq.gz		Artificial_Sputum	3	0	reverse
MB_1	SRX1607054_T1.fastq.gz		Middlebrook	1	0	reverse
MB_2	SRX1607055_T1.fastq.gz		Middlebrook	2	0	reverse
MB_3	SRX1607056_T1.fastq.gz		Middlebrook	3	0	reverse

Optional Contrast Table

contrast_ref.tsv

contrast1	contrast2
Artificial_Sputum	Middlebrook

Output

1. fastp directory containing adaptor-trimmed RNA-Seq files and QC results.
2. read_counts directory containing:
   1. ref_gene_df.tsv: table of genes in the annotation.
   2. gene_counts.tsv: raw read counts per gene.
   3. cpm_counts.tsv: size factor scaled counts per million (CPM).
   4. rpkm_counts.tsv: size factor scaled and gene length-scaled counts, expressed as reads per kilobase per million mapped reads (RPKM).
3. PCA_samples directory containing principal component analysis results.
4. diff_expr directory containing differential expression results.
5. bigwig directory containing BigWig files.
6. bwa_aln directory containing BAM files.

Slurm Example

#!/usr/bin/bash
#SBATCH --job-name=chienlab-rnaseq-ba   # Job name
#SBATCH --partition=cpu            # Partition (queue) name
#SBATCH --ntasks=24                   # Number of CPUs
#SBATCH --nodes=1                       # Number of nodes
#SBATCH --mem=64gb                     # Job memory request
#SBATCH --time=06:00:00               # Time limit hrs:min:sec
#SBATCH --output=logs/chienlab-rnaseq-ba_%j.log   # Standard output and error log

# Load modules

module load nextflow/24.04.3 conda/latest

# Run pipeline

nextflow run baldikacti/chienlab-rnaseq -r v0.1.0 \
    --data_dir /path/to/fastq \
    --sample_file /path/to/reference.tsv \
    --ref_genome /path/to/organism.fasta \
    --ref_ann /path/to/annotation.gff \
    --cont_tabl /path/to/contrast_ref.tsv \
    --outdir /path/to/results \
    -profile conda \
    -resume

Citation

This software has been used in the following publication. If you use this software in your publication, please cite one of the following.

Aldikacti, B., Putun, H., Sarsani, V., Zeinert, R., Flaherty, P., & Chien, P. (2026). Stress testing reveals selective vulnerabilities in protein homeostasis. Cell reports, 45(2), 116892. https://doi.org/10.1016/j.celrep.2025.116892

@software{berent_aldikacti_2025_17809427,
  author       = {Berent Aldikacti},
  title        = {baldikacti/chienlab-rnaseq: v0.1.0pub Publication
                   Release
                  },
  month        = dec,
  year         = 2025,
  publisher    = {Zenodo},
  version      = {v0.1.0pub},
  doi          = {10.5281/zenodo.17809427},
  url          = {https://doi.org/10.5281/zenodo.17809427},
  swhid        = {swh:1:dir:83cd7ba8cf44d65dd4ca06835dd41c78a537bbf8
                   ;origin=https://doi.org/10.5281/zenodo.17809426;vi
                   sit=swh:1:snp:4a4d4113500fcbb9ab49c6438a8a71bee8e3
                   24b9;anchor=swh:1:rel:fe51489f9cb75637fc90128b8d6b
                   9a708829c9a0;path=baldikacti-chienlab-
                   rnaseq-e0b3d68
                  },
}