Quartet RSeQC Report is a quality assessment tool for RNA-seq data. It contains two parts: workflow and report. The workflow command takes raw reads (in FASTQ format), produces a set of qc result files from them. and you can use report command to report the results finally. We strongly recommend you to use the whole pipeline with docker to analyze your raw data and generate the report. See Whole pipeline for more details. If you only want to generate the report from the expression table, see Only report for more details.
see more details on QDP Docs.
you need to get the tag name from here, and replace the [tag_name] with the tag name. such as v0.2.4-15cd635b
docker pull ghcr.io/chinese-quartet/quartet-rseqc-report:[tag_name]
We assume you have the folloing files in the /report directory which is mounted to the docker container.
docker run -v <your-local-directory>:/report --entrypoint bash -it ghcr.io/chinese-quartet/quartet-rseqc-report:[tag_name]
# If you get a bash shell like this, it means you have successfully run the docker image
# root@af1ae467b246:/data#
NOTE:
- We assume you have the following files in the /report directory:
fpkm.csv,count.csv,metadata.csv- You must be sure that you are in the docker container
The fpkm.csv and count.csv are the expression table, and the metadata.csv is the phenotype table.
Get the example files from here: fpkm.csv, count.csv, metadata.csv
mkdir /report/output
bash /venv/bin/exp2qcdt.sh -e /report/fpkm.csv -c /report/count.csv -m /report/metadata.csv -o /report/output
After the above command, you will get the following files in the /report/output directory in the docker container or /output directory in your local machine.
multiqc /report/output -t quartet_rnaseq_report
After the above command, you will get the final report file multiqc_report.html in the /report/output directory in the docker container or /output directory in your local machine.
You need to install Docker first.
git clone https://github.com/chinese-quartet/quartet-rseqc-report
cd quartet-rseqc-report
bash build-docker.sh
# After build docker image, you can run the docker image
docker run -it --rm quartet-rseqc-report:<tag_name> --help- Bash
- Python3 >= 3.7
- pip3
- Java
- R >= 3.6.3
# For Linux
conda create -c conda-forge -c bioconda -c anaconda -n quartet-rseqc-report python=3.9 openjdk=8.0.312 r-base=3.6.3 blas lapack cxx-compiler conda-pack gfortran_linux-64
# For Mac
conda create -c conda-forge -c bioconda -c anaconda -n quartet-rseqc-report python=3.9 openjdk=8.0.312 r-base=3.6.3 blas lapack cxx-compiler conda-pack
# Activate conda environment
conda activate quartet-rseqc-report
# Clone the repo
git clone https://github.com/chinese-quartet/quartet-rseqc-report
cd quartet-rseqc-report
# Build the environment and compile the quartet-rseqc-report
make all
source .env/bin/activate
java -jar target/uberjar/quartet-rseqc-report-*-standalone.jar -hPlease access Quartet Service for more details
copm-cli install -n quartet-rseqc-report -V v0.2.4 -d pluginsQuartet QC Report for RNA-Seq Data developed by Jun Shang <exp2qcdt & report>
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This program and the accompanying materials are made available under the terms of the Eclipse Public License 2.0 which is available at http://www.eclipse.org/legal/epl-2.0.
This Source Code may also be made available under the following Secondary Licenses when the conditions for such availability set forth in the Eclipse Public License, v. 2.0 are satisfied: GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version, with the GNU Classpath Exception which is available at https://www.gnu.org/software/classpath/license.html.