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Introduction

Requirements for your data and metadata

Analyze your data on Quartet Data Portal

See more details on Step by Step Guide

Analyze your data on your own server

Quartet RSeQC Report is a quality assessment tool for RNA-seq data. It contains two subcommands: workflow and report. The workflow command takes raw reads (in FASTQ format), produces a set of qc result files from them (More details on RNA-Seq QC for Quartet). and you can use report command to report the results finally (More details on QC Report for Quartet RNA-Seq).

Assuming your data files are in the /your-dir directory.

  1. Prepare a set of subdirectories

    mkdir -p /your-dir/fastq_screen /your-dir/hisat2 /your-dir/gtf /your-dir/results /your-dir/raw-data /your-dir/report

  2. Download the dependency files

    # 1. Download reference genomes for `fastq_screen` (More details on https://figshare.com/articles/online_resource/fastq_screen_zip/22121078)
wget https://figshare.com/ndownloader/files/39310673 -O /your-dir/fastq_screen/fastq_screen.zip
unzip /your-dir/fastq_screen/fastq_screen.zip -d /your-dir/fastq_screen

# 2. Download GTF file (More details on https://figshare.com/articles/online_resource/Homo_sapiens_GRCh38_93_gtf/22117475)
wget https://figshare.com/ndownloader/files/39308702 -O /your-dir/gtf/Homo_sapiens.GRCh38.93.gtf

# 3. Download Hisat2 index files (More details on https://figshare.com/articles/online_resource/hisat2_zip/22120538)
wget https://figshare.com/ndownloader/files/39310418 -O /your-dir/hisat2/hisat2.zip
unzip /your-dir/hisat2/hisat2.zip -d /your-dir/hisat2

  3. Place your data files into /your-dir/raw-data directory

  4. Pull docker image

    More versions on Docker Registry

    docker pull ghcr.io/chinese-quartet/quartet-rseqc-report:v0.2.4-15cd635b

  5. Generate qc result files by workflow command

    docker run -d -v /your-dir:/data -it ghcr.io/chinese-quartet/quartet-rseqc-report:v0.2.4-15cd635b workflow -i /data/hisat2 -g /data/gtf/gencode.v36.annotation.gtf -s /data/fastq_screen/fastq_screen.conf --output-dir /data/results --r1 /data/raw-data/example_R1.fq.gz --r2 /data/raw-data/example_R2.fq.gz

  6. Report the results

    docker run -d -v /your-dir:/data -it ghcr.io/chinese-quartet/quartet-rseqc-report:v0.2.4-15cd635b report -d /data/results -m /data/metadata.csv --output-dir /data/report

  7. Find your QC report in /your-dir/multiqc_report.html

Last update: 2023-06-20
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