rTea (RNA Transposable Element Analyzer)

rTea is a computational method to detect transposon-fusion RNA.

• Citation: Pan-cancer analysis reveals multifaceted roles of retrotransposon-fusion RNAs

Overview

We developed rTea to detect TE-fusion transcripts from short-read RNA-seq data. We utilized multiple features from aligned reads, such as base quality of clipped sequences, percentage of multi-mapped reads, and matching score of reads to TE sequences to filter out false positives caused by nonspecifically mapped reads.

Demo and result files

Users can try rTea on a demo data set and can check the output at https://gitlab.aleelab.net/junseokpark/rTea-results

Installation

rTea runs on a Linux-based operating system with certain prerequisite software. Here is a list of the software you should install before you start using rTea.

• System software for Ubuntu 18.04 LTS

  apt-get update && apt-get install -y \
  cmake \
  libxml2-dev \
  libcurl4-openssl-dev \
  libboost-dev \
  gawk \
  libssl-dev \
  pigz \
  htop \
  iputils-ping

• Before installing rTea, you'll also need to set up the prerequisite software and environment variables (ENV).

  • fastp
  • HISAT2 (>= v2.1.0)
  • samtools (>= v1.9)
  • HTSlib (>= v1.9)
  • Scallop (>= v0.10.4)
  • bamtools (>= v2.5.1)

    # Bamtools environment
    # BAMTOOL_HOME is installed directory
    PKG_CXXFLAGS="-I$BAMTOOL_HOME/include/bamtools"
    PKG_LIBS="-L$BAMTOOL_HOME/lib -lbamtools"

  • bwa (>=0.7.17)

• R (==3.6.2) and the necessary R software should be installed.

  
  R -e "install.packages('XML', repos = 'http://www.omegahat.net/R')"
  R -e "install.packages(c( \
     'magrittr', \
     'data.table', \
     'stringr', \
     'optparse', \
     'Rcpp', \
     'BiocManager' \
   ))"

R -e "BiocManager::install(c( \ 'GenomicAlignments', \ 'BSgenome.Hsapiens.UCSC.hg19', \ 'BSgenome.Hsapiens.UCSC.hg38', \ 'EnsDb.Hsapiens.v75', \ 'EnsDb.Hsapiens.v86' \ ))"

* Download GRCh38 [genome_snp_tran](https://genome-idx.s3.amazonaws.com/hisat/grch38_snptran.tar.gz)

## Use Docker for Installation
Build a Docker file and run ``rTea`` in the Docker container.
```bash
DOCKER_BUILDKIT=1 docker build -t rtea .

Use Singularity for Installation

After creating a Docker image for rTea, convert it to Singularity.

docker save -o rTea.tar rtea:latest
singularity build rTea.simg docker-archive://rTea.tar

Running rTea

If you are using Docker as your runtime environment, run the Docker image to execute rTea.

docker exec -it -v ${GENOME_SNP_TRAN_DIR}:/app/rTea/hg38/genome_snp_tran rtea bash

If the runtime environment is Singularity, execute the Singularity image to run rTea.

singularity shell -B ${GENOME_SNP_TRAN_DIR}:/app/rTea/hg38/genome_snp_tran \
    rTea.simg

rTea supports paired-end FASTQ files and a BAM file as input. For FASTQ file input, use the following command:

rTea.sh \
        ${R1.fq}.gz \
        ${R2.fq}.gz \
        $SAMPLE_NAME \
        $GENOME_SNP_TRAN_DIR \
        $NUMBER_OF_CORES \
        $OUT_DIR \
        hg38 \
        resume

For BAM file input, please use the following command:

rnatea_pipeline_from_bam \
        ${BAM} + \
        $SAMPLE_NAME \
        $GENOME_SNP_TRAN_DIR \
        $NUMBER_OF_CORES \
        $OUT_DIR \
        hg38

Output file

Licenses

Contacts

Junseok Park Boram Lee