R Analysis

Before beginning the analysis in R, import the kallisto quantification directories to your local machine.

The quant/ directory should have the following tree structure:

quant/
├── A375_1
│   ├── abundance.h5
│   ├── abundance.tsv
│   └── run_info.json
├── A375_2
│   ├── abundance.h5
│   ├── abundance.tsv
│   └── run_info.json
├── A375_3
│   ├── abundance.h5
│   ├── abundance.tsv
│   └── run_info.json
├── A549_1
│   ├── abundance.h5
│   ├── abundance.tsv
│   └── run_info.json
├── A549_2
│   ├── abundance.h5
│   ├── abundance.tsv
│   └── run_info.json
├── A549_3
│   ├── abundance.h5
│   ├── abundance.tsv
│   └── run_info.json
├── ctrl_1
│   ├── abundance.h5
│   ├── abundance.tsv
│   └── run_info.json
├── ctrl_2
│   ├── abundance.h5
│   ├── abundance.tsv
│   └── run_info.json
└── ctrl_3
    ├── abundance.h5
    ├── abundance.tsv
    └── run_info.json

tarzip the dirctory so we can move it to your bactsrv directory.

tar -zcvf quant.tar.gz quant/

Using scp, transfer the file to your own bactsrv account:

scp quant.tar.gz USERNAME@bactsrv.nuigalway.ie:/home/USERNAME

Close the connection to lugh and move to your local machine. Create a directory in your home directory and move there:

mkdir ~/RNA-Seq/
cd ~/RNA-Seq

Now download the tar file and unzip it.

scp USERNAME@bactsrv.nuigalway.ie:/home/USERNAME/quant.tar.gz ./ && tar -xvf quant.tar.gz

Create a sample table file. Save is as samples.csv

sample,condition,replicate
ctrl_1,control,1
ctrl_2,control,2
ctrl_3,control,3
A549_1,lung,1
A549_2,lung,2
A549_3,lung,3
A375_1,melanoma,1
A375_2,melanoma,2
A375_3,melanoma,3

Rmd Document

Download the Rmd file here: https://github.com/BarryDigby/barrydigby.github.io/blob/master/RNA-Seq/MA5512.Rmd.

or follow along with the Published HTML here: https://rpubs.com/BarryDigby/747584

Genomic Data Analysis II

R Analysis

Rmd Document