Corresponding lecture

Lecture 2 - Ultra-fast read mapping with Kallisto


Homework #1: DataCamp Intro to R course (~2hrs) is due today!


In our lecture, we covered the basics for running Kallisto with a single sample. However, you will rarely, if ever, be dealing with a single sample. In this lab, we’ll work through how to automate alignments and other command-line work using shell scripts and ‘for loops’. To keep the lab moving along, we’ll work with very small fastq files (see below)

Files you’ll need for this lab

subsampled fastq files - This is the course dataset, but each file has been subsampled to retrieve only 10,000 reads per sample.

shell script – To carry out read mapping and QC analysis for multiple samples.

Follow along

Bash basics - this is the code I’ll be running and discussing in lab today. You can copy/paste lines from this page to follow along.