Downloading today’s files
On the desktop, make a folder called RNA-seq. Make another folder called sleuth_files inside RNA-seq.
cd ~/Desktop
mkdir RNA-seq
cd RNA-seq
mkdir sleuth_files
Download the zipped file in the kallisto dropbox link below. From the sleuth dropbox link,
only download the hi_seq.txt file if you are not jumping straight into the sleuth part of the
tutorial. Unzip the kallisto dropbox file into the ~/Desktop/RNA-seq folder made earlier. Move
the hi_seq.txt file into ~/Desktop/RNA-seq.
For Kallisto files: https://www.dropbox.com/sh/n84n0n1i3sdi552/AAACLGmpM6cHiNF_MnXfwONDa?dl=0
For Sleuth files: https://www.dropbox.com/sh/diu7c7kmxec08bz/AAAZnRTjA2mlQwdnt060os5Ca?dl=0
To install Kallisto (bash)
Change directory to the Desktop.
cd ~/Desktop
Download kallisto by running the command below. ‘linux’ can be replaced with ‘mac’, or ‘windows’ depending on the system.
wget https://github.com/pachterlab/kallisto/releases/download/v0.45.0/kallisto_linux-v0.45.0.tar.gz
Unpack the gzipped file using;
tar -zvxf kallisto_linux-v0.45.0.tar.gz
By running ‘ls’, we a new folder in the Desktop. This folder contains the Kallisto program. Enter this folder by typing;
cd kallisto_linux-v0.45.0
To make linux recognize the kallisto program and to make it executable from any folder, copy the
kallisto program into /usr/local/bin/. The program will have to be made into an executable.
sudo cp kallisto /usr/local/bin/
cd /usr/local/bin/
sudo chmod +x kallisto
To install Sleuth (Rstudio)
rhdf5 will be required from bioconductor to run sleuth. Occasional first time installers may also need fs.
BiocManager::install("rhdf5")
install.packages("fs")
Devtools should have been previously installed. Install sleuth using:
devtools::install_github("pachterlab/sleuth")
library(sleuth)
If devtools are missing, they can be installed by:
install.packages("devtools")
To learn more
Kallisto has an offical page here: https://pachterlab.github.io/kallisto/
Sleuth has an official page here: https://pachterlab.github.io/sleuth/
(modified from https://pachterlab.github.io/kallisto/source, and https://scilifelab.github.io/courses/rnaseq/labs/kallisto)