This five-day course provides an introduction to the concepts and vocabulary of Next Generation Sequencing (NGS) with an emphasis on common protocols, tools and file formats used in NGS data analysis. Subjects covered include quality assessment and manipulation of raw NGS sequences (FastQC, cutadapt), read mapping (bwa, bowtie2), the Sequence Alignment Map (SAM) format, and tools for manipulating BAM files (samtools, bedtools). Participants will gain hands-on experience using these and other NGS tools in the Linux command line environment at TACC, as well as exposure to the many bioinformatics resources TACC makes available.
Preferred or Prerequisite Skills:
None. UNIX/Linux command line experience is not required, and becoming familiar with how to use the command line for NGS analysis will be a major focus of this course. However, to get a head start on developing this important skill you can register for our Introductory UNIX short courses.
Computer Requirement:
In order to participate fully in the hands-on exercises students should have their own laptop computer with an SSH client program. Macs have SSH available in the Terminal application. Recent Windows versions have an SSH client built into its PowerShell and Command Prompt programs, or PuTTy can be used if SSH is not available. A TACC Account and UT EID are also required. To obtain a UT EID, go here. To sign up for a TACC account, go here.
If you use the UT ProCard for payment of courses, please be aware that you can only charge ONCE per 24 hour period. Any attempts to charge more courses will fail, and you will not be registered.
For example, you may add one to many courses for one student into your shopping cart at any one time, and charge them to the ProCard, and you should receive a "registration successful!" page at the end. This is because you registered ONCE for ONE student. If you attempt to register and pay again, for example, for a different student, this will trigger the UT ProCard security system to stop payment, and your registration will not be successful. A page stating this fact will occur after you attempt to process payment. It looks a lot like the "registration was successful" page.
Ways to avoid this are: use the ProCard after 24 hours have passed, or the student may use their credit card and be reimbursed later through the usual UT accounting methods, or process the registration with an IDT, otherwise known as an Interdepartmental Transfer (talk to someone in your department that handles the accounts).