Pipeline for psoralen sequencing analysis
Installation:
sudo apt update
sudo apt-get install -y openjdk-11-jdk build-essential gcc zip unzip zlib1g-dev make
curl -s https://get.sdkman.io | bash
source "/home/ubuntu/.sdkman/bin/sdkman-init.sh"
sdk install java 17.0.10-tem
curl -s https://get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
nextflow -version #tested with nexflow 24.10.5
git clone https://github.com/gwickh/psoraseq.git
Usage:
Run the pipeline with alignment:
nextflow run psoraseq/main.nf --reads_dir <directory_with_reads> --bowtie2_ref <path_to_index> --output_dir <output_directory> --ori_centric_offset <ori_position>
Skip alignment and run downstream processes:
nextflow run psoraseq/main.nf --skip_alignment --output_dir <output_directory>
Options:
--reads_dir Path to directory containing paired reads.
Reads should be in the format {name}_R{1/2}.{fastq/fastq.gz}
(OPTIONAL) Reads with the same name but containing the prefix "sample" will be plotted relative to reads prefixed as "control"
--bowtie2_ref Path to Bowtie2 index or reference .fasta file to make new index
--output_dir Path to output directory.
Directory will be created if does not already exist
--ori_centric_offset (OPTIONAL) Numeric offset to make coordinates origin-centric (default: 0).
--smoothing_window (OPTIONAL) Smooth trendline with binsized sliding window (default: 1)
--skip_alignment (OPTIONAL) Skip alignment step and use precomputed BAM/BAI files in output directory.
--help Display help message.
Example:
nextflow run psoraseq/main.nf --reads_dir psoraseq/test_files/test_reads/ --bowtie2_ref psoraseq/test_files/e_coli_K12_ref --output_dir output_test --ori_centric_offset 3925744 --smoothing_window 100