Day 3. Data Formats and Visualization

A large fraction of biological science in these days involves analysis of genomic data.

There are many de facto standards for representing genomic data, including but not limited to, FASTA, FASTQ, SAM/BAM, VCF, GTF, and BED formats. The ability to read and manipulate data files stored in these formats is one of the key skill sets needed for genome scientists.

Effective visualization of the genomic data and its analysis outcome is a key component for successful communication in the research community handling a large amount of genomic data.

Today, we will learn the widely used genomic data formats and practice how to read and manipulate the data in these formats. We will also learn the basics of data visualization with practice on real data.


Schedule:

Session Time Topics
I 9:00-10:15 AM Mini-Practice : FASTQ File Manipulation
  10:15-10:30AM Coffee Break
II 10:30-11:15 AM Lecture : Data Formats and Conversions
III 11:15-12:00 AM Mini-Practice: Select a subset of variant/genotype calls
  12:00-1:00PM Lunch
IV 1:00-2:15 PM Practice : Analysis with Genomic Data Formats
  2:15-2:30 PM Coffee Break
V 2:30-4:00 PM Visualization: Overview and Practice


Instructors:

Hyun Min Kang (HMK)
Jacob Kitzman (JK)


Topics:

I) Mini-Practice : FASTQ File Manipulation [1:15 hr] HMK

—- Coffee Break [15 mins] —

II) Lecture : Overview of Genomic Data Formats and Conversions [0:45 hr] JK

III) Mini-Practice: Select a subset of variant/genotype calls [0:45 hr] JK

—- Lunch Break [1 hr] —

IV) Practice : Analysis with Genomic Data Formats [1:15 hr] HMK

—- Coffee Break [15 mins] —

V) Visualization: Overview and Practice [1:30 hr] JK

—- End/Wrap-Up —


Reference material

Referene Commands and Glossary