1  Downloading sequencing data

1.0.1 How to access the “shell” and RStudio

This allows you to use RStudio from a web browser and access a computing server.

Access the RStudio website

Access options, choose either to connect… - from a computer in a Unimail computer room - from a laptop/tablet connected to the unine wifi - from home through the UNINE VPN GlobalProtect (requires installing the software provided by SITEL)

Then, use a web browser to navigate to this site here: http://legcompute3.unine.ch:8787

• Username & password: check the course docs for your username and password

To transfer a file to the server:
Find the “Files” tab (typically bottom right of the RStudio screen), click on “Upload” and select “Choose File”. The file will upload and you can spot it now under “Files”.

To recover a file from the server and save it on your computer:
Find the “Files” tab (typically bottom right of the RStudio screen), select the file(s) to download, click on “More” and then “Export…”. This will get you to the download stage

1.1 Download data (and repo from github)

git clone https://github.com/cmaslard/bioinformatic_tools_mcom_analyse.git

Open the files in data/sequencing_data/ bacteria_16S or fungi_ITS

What are the names of the files?

help: gunzip *.fastq.gz because the files are compressed.

What do the first lines look like?

help: head 20_bk.effective.fastq