TEtranscripts Parallel Pipeline

This repository provides a reproducible, parallelized pipeline for quantifying transposable elements and gene expression from RNA-seq BAM files using TEtranscripts.

Features

• Automated installation of dependencies (Conda, Python, R, TEtranscripts)
• Parallel processing of multiple BAM files using GNU parallel
• TE and gene expression quantification in a single output directory

Requirements

• Bash shell
• wget, curl, parallel, unzip
• Internet access for downloading dependencies

Usage

##Clone the GitHub Repository###
git clone https://github.com/Ali-mhm/TEtranscripts_Multi_thread.git
cd TEtranscripts-pipeline

##Make the Script Executable###
chmod +x run_TEtranscripts_pipeline.sh

##(Optional) Edit Configuration##
ENV_NAME="te_env"                # Conda environment name
THREADS=4                        # Number of threads for parallel processing
BAM_DIR=~/testdata_PE           # Directory containing your BAM files
OUTPUT_DIR=~/output1            # Output directory

##Run the Pipeline##
./run_TEtranscripts_pipeline.sh

manually step-by-step workflow

Install GNU parallel

echo "Installing GNU parallel..."
sudo apt-get update -qq
sudo apt-get install -y parallel

Install Anaconda
wget https://repo.anaconda.com/archive/Anaconda3-2024.02-1-Linux-x86_64.sh
bash Anaconda3-2024.02-1-Linux-x86_64.sh -b -p $HOME/anaconda3
conda install -c conda-forge mamba

Create and activate conda environment

mamba create -n tetranscript python=3.7 -y
conda activate tetranscript

Install dependencies

mamba install -c bioconda samtools bedtools -y
mamba install -c conda-forge r-base=4.4.0 -y

Install TEtranscripts

wget https://github.com/mhammell-laboratory/TEtranscripts/archive/refs/heads/master.zip
unzip master.zip
cd TEtranscripts-master
pip install .
cd ..

Download TE GTF

curl -L -o TE_GTF.zip "https://www.dropbox.com/scl/fo/jdpgn6fl8ngd3th3zebap/ACdZkShDC1au-OckIipI5kM/TEtranscripts/TE_GTF?rlkey=41oz6ppggy82uha5i3yo1rnlx&dl=1"
unzip TE_GTF.zip -d TE_GTF
gunzip TE_GTF/*.gz

Download and unzip GENCODE annotation

wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/gencode.v44.annotation.gtf.gz
gunzip gencode.v44.annotation.gtf.gz

check the chromosome name style

head gencode.v44.annotation.gtf | cut -f1 | sort | uniq
head hg38_rmsk_TE.gtf | cut -f1 | sort | uniq

Fix chromosome names (if needed)

sed 's/^chr//' TE_GTF/hg38_rmsk_TE.gtf > TE_GTF/hg38_rmsk_TE.fixed.gtf
sed 's/^chr//' gencode.v44.annotation.gtf > gencode.v44.annotation.fixed.gtf

Define TEcount wrapper

run_tecount() {
    local BAM_FILE="$1"
    local SAMPLE_NAME
    SAMPLE_NAME=$(basename "$BAM_FILE" .bam)

    echo "Running TEcount for $SAMPLE_NAME..."

    TEcount \
        -b "$BAM_FILE" \
        --GTF "$GTF" \
        --TE "$TE_GTF" \
        --format BAM \
        --stranded no \
        --mode multi \
        --project "$SAMPLE_NAME" \
        --outdir "$OUTPUT_DIR" \
        --verbose 3
}

export -f run_tecount

Run TEcount in parallel for all BAM files

find "$BAM_DIR" -name "*.bam" | parallel -j 4 run_tecount