Tutorial

We create this small test dataset for you to test Mirror-seq quick-and-easy.

Install Docker

Please reference the Install Docker part in Quick Start

Download Dataset

• Download Read 1, Read 2, and Bismark index to the directory you selected.
• Unzip control.zip into the same directory.

Run

• Open terminal if you are not already in a terminal
• Change directory to the directory with test dataset.
• Run the command. (It will download the latest Docker image (1GB) and run Mirror-seq analysis tool.)

docker pull zymoresearch/mirror-seq
docker run --rm -v `pwd`:/workspace zymoresearch/mirror-seq -1 test_R1.fastq.gz -2 test_R2.fastq.gz -g control --bed --non_directional

Note: We add --non_directional argument in docker run because the dataset is non directional library prep. When you run your own data, you don't need this argument if you use directional library prep.

Result Files

It should take <1 minute to run it. Here are the expected result files:

• Processed Fastq Files Fastq files with adapter, quality trimmed, and filled-in nucleotides.
  • test_R1_val_1.fq.gz and test_R1_val_2.fq.gz are adapter and quality trimmed fastq files generated by Trim Galore!.
  • test_R1_trimmed.fastq.gz and test_R2_trimmed.fastq.gz are the final trimmed files with filled-in nucleotides trimming. These files are used for downstream analysis.
  • test_R1.fastq.gz_trimming_report.txt and test_R2.fastq.gz_trimming_report.txt are the trimming logs generated by Trim Galore!.
• Alignment Files
  • test_R1.fastq_pe.bam The sorted BAM file. It includes Bismark's special tags for methylation data.
  • test_R1.fastq_pe.bam.bai is the index file for test_R1.fastq_pe.bam.
  • test_R1.fastq_PE_report.txt is the alignment log file generated by Bismark.
• Hydroxymethylation Ratio Files
  • test_R1.fastq_pe_CpG.csv.gz is the result table of all detectable CpGs. Please reference README for details.
  • test_R1.fastq_pe_CpG.bed.gz is the browser tack that you can load in genome browsers. It is generated because we give --bed argument in the docker run command. Please reference README for details.