ImmuAge Pipeline

Version: 1.0

This pipeline is designed for processing and analyzing RNA-seq data, with a focus on immunological aging studies.

Prerequisites

• Python 3.x
• R (for certain modules)
• Various bioinformatics tools (STAR, featureCounts, RSEM, etc.)

Installation

[Provide installation instructions here]

Usage

python immuage_pipeline.py [options]

Options

• -f, --readFolder: Folder with RNA-seq data (gzipped fastq files)
• -e, --threads: Number of threads for Parafly (Default: 8)
• -p, --Parallel: Use Parafly for parallel processing (Default: True)
• -s, --starindex: STAR index (Default: '/home/maolp/mao/Ref/hg38/genome')
• -m, --Module: Processing module to run (Default: 'RA')
• -g, --genome: Path to genome reference (Default: '/home/maolp/mao/Ref/')
• -u, --gtf: Path to GTF file (Default: '/home/maolp/mao/Ref/Homo_sapiens/UCSC/hg38/Annotation/Genes.gencode/genes.gtf')
• -c, --count: Counting method (Default: 'featureCounts')
• -a, --alignmethods: Alignment method (Default: 'hisat2')
• -t, --alignthreads: Number of threads for alignment (Default: 40)
• -x, --rsemindex: RSEM index (Default: '/home/maolp/mao/Ref/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/HG38RSEM/HG38RSEM')
• -l, --less: Only process a subset of files (Default: True)
• -n, --globname: Global name for the run (Default: 'NEW')
• -w, --rmarkdown: Path to R Markdown file (Default: '/home/maolp/mao/Codeman/Immuagepipeline/Immuageclock_Run02_PCA.Rmd')
• -r, --rcut: Path to R script (Default: '/home/maolp/mao/Codeman/Immuagepipeline/Immuage_Rmain.R')
• --coldata: Path to coldata file (Required)
• --add: Add all, part, or none (Default: 'ap')
• --health: Update old program (Default: False)
• --rootdir: Root directory (Default: '/data2/users/maolp/Immu_age/Immuageroot')
• --pipepath: Pipeline directory (Default: '/home/maolp/mao/Codeman/Immuagepipeline')
• --resmode: Result mode (Default: 'train_pre')
• --config: Path to config file

Modules

The pipeline includes several modules that can be specified using the -m option:

• S1: FastQC
• S2: TrimQC
• S3_1: STAR indexing
• S3: Alignment
• S14: QC to Count
• S34: Align to count
• S5_1: R Markdown
• S5: Normalization
• S6: Regression
• S78: CircRNA HLA TCR
• S7: TCR HLA
• S8cir: CircleRNA
• RAR: Run all real
• RA: Run all (Default)

Example

python immuage_pipeline.py -f /path/to/fastq/files -m S14 --coldata /path/to/coldata.txt

This command will run the pipeline from QC to Count on the fastq files in the specified folder.