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Quick Start

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Hunter Chung edited this page Jul 9, 2016 · 6 revisions

The Qucik Start is the easiest 1 step analysis. Just type in the command below. You will find results in your workspace in several hours. We created a Docker image to solve the dependency problem and you can use either Windows, MacOS, or Linux to run the analysis.

0 - Install Docker

You may think I am lying (It's two steps!!!), but Docker is the only prerequisite of Quick Start. Follow Docker official installation instructions to install Docker (Windows, MacOS, Linux).

Note: For Earlier verisons of Windows (Windows 8, 7 etc.) please use the [Docker Toolbox] (https://www.docker.com/products/docker-toolbox). And this is the [link] (https://docs.docker.com/toolbox/overview/) to follow to install Docker Toolbox.

1 - Run

Please don't go away. I really mean running the command. You need to create a workspace directory (<YOUR WORKSPACE>) and put the following files inside:

  • Read 1 and Read 2 Fastq files.
  • Bisulfite converted Bowtie2 genome index created by Bismark. We provide human (hg19) and mouse (mm10) indexes in our cloud. Unzip the file to the workspace.

Run this command in your console.

docker run -d -v <YOUR WORKSPACE>:/workspace \
  zymoresearch/mirror-seq \
  -1 <READ 1 FILENAME> -2 <READ 2 FILENAME> \
  -g <GENOME INDEX FOLDER NAME> --bed

Notes:

Although it is super easy to run the analysis tool, there are several things you need to know in order to run it smoothly.

  • The alignment part is memory and CPU intensive. Bismark, the aligner we used in our tool, suggests at least 5 cores and > 16GB of RAM.
  • Usually Fastq files are several GB with compression. In the first trimming part, the tool may need up to 3X large as the original input. Please make sure your workspace has enough storage space.
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