Week 2

Agenda for (01/19/2022)

• Introduction to sequencing technologies and bioinformatic tools

• Troubleshoot conda and jupyter-lab related issues

• Go over why we use pandoc in this course

• Brief introduction to Markdown

• Install some necessary tools using conda:

  • sra-tools

  • fastqc

  • bbmap

• Group activity to download and test tools with sample datasets

• Assignments:

  • Assignment 2

  • Reading assignments

Introduction to sequencing technologies and bioinformatic tools

See the Powerpoint presentation given in class. It will be uploaded to Blackboard as well.

Troubleshoot conda and jupyter-lab related issues

We will revisit the exercises from last week and I will help you along with installing and troubleshooting other issues related to setting up the computing environment to get you ready for the exercises.