Informatics for High-throughput Sequencing Data Analysis 2017 Pre-Work

Install these tools before the workshop:

1) A robust text editor.

2) A file decompression tool.

  • For Windows/PC – 7zip.
  • For Linux – gzip.
  • For Mac – already there.

3) A robust internet browser such as Firefox or Safari (Internet Explorer and Chrome are not recommended because of Java issues).

4) Java -The visualization program that we will be using (IGV) requires Java. Check if you have Java installed: https://www.java.com/verify/ and download Java if you do not have it installed (Java 8).

5) Integrative Genomics Viewer 2.3 (IGV) - Once java is installed, go to http://www.broadinstitute.org/igv/ and register in order to get access to the downloads page. Once you have gained access to the download page, click on the appropriate launch button that matches the amount of memory available on your laptop (if you have space, 1.2GB is good, more is better).

Note Chrome does not launch “java webstart” files by default. Instead, the launch buttons below will download a “jnlp” file. This should appear in the lower left corner of the browser. Double-click the downloaded file to run.

Windows users: To run with more than 1.2 GB you must install 64-bit Java. This is often not installed by default even with the latest Windows 7 machines with many GB of memory. In general trying to launch with more memory than your OS/Java combination supports will result in the obscure error “could not create virtual machine”.

6) SSH client - Mac and Linux users already have a command line ssh program that can be run from the terminal. For Windows users, please download PuTTY.

7) SCP/SFTP client - We will be moving data from the servers to the student laptops for visualization. Mac and Linux users already have a command line scp and sftp program. For Windows users, please install WinSCP.

8) A PDF viewer (Adobe Acrobat or equivalent).

Do these tutorials before the workshop

1) R Preparation tutorials: You are expected to have completed the following tutorials in R beforehand. The tutorial should be very accessible even if you have never used R before.

2) UNIX Preparation tutorials:

3) Sequencing Terminology

Before coming to the workshop, read these: