6.3 Fetch public data from miRBase and SRA

miRBase and MirGeneDB

Download Reference microRNA data from miRBase

First, let’s create a folder to store the reference datasets:

Now move to the reference folder and download the miRBase datasets using wget in an Interactive session or (see below) use a PBS Pro script.

OPTION #1: Use interactive session to run the following commands:

Fetch microRNA mature sequences:

Fetch hairpin sequences:

Fetch the genomic coordinated for precursors and mature sequences:

OPTION #2: submit the following PBS Pro script to the cluster. Let’s

1. copy the script to download miRBase files;

2. move to the reference folder; and

3. print the content of the launch_download_miRBase.pbs script with the code below:

submit the script to the HPC cluster:

monitor progress of job:

Fetch public small RNA-seq data

Today we will download small RNA-seq data from the ENA (European Nucleotide Archive).

Manuscript: https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004188

Open

STEP 1 : Find where the data is available for download in the above manuscript

• Click on the link above and search for “accession”, “Data availability”, “BioProject ID”, “GEO accession code” or “Array Express” identifier.

• If, only an Array Express accession code is available, then go to https://www.ebi.ac.uk/biostudies/arrayexpress and search for the Array Express identifier. Browse the database to located the identifier for ENA.

• Hint: it will take a couple of clicks to open multiple pages to find the identifier for the data deposited in ENA.

Open

Which is the Array express identifier noted in the above manuscript and to which ENA identifier it relates to?

STEP 2: Search for data for the identified BioProject ID at the European Nucleotide Archive (ENA) database

• Go to https://www.ebi.ac.uk/ena/browser/home and search for the BioProject ID using the search option on the top right corner and click on ‘view’:

STEP3: Select FASTQ files (tick boxes next to the file names) and click on “Get download script”. NOTE: the Script Name will be different for each person downloading the bash script (e.g., )

• STEP 4: Download the metadata information for the study in TSV (Tab-Separated Values) format:

Open the file using an app for Text files (e.g., TextEdit, NotePad, etc):

• STEP 5: Select FASTQ files (tick boxes next to the file names) and click on “Get download script”. This will download a bash script (e.g., )

• Open the downloaded ena file using TextEdit (NotePad or similar app). The downloaded script looks like this:

Now using the TextEdit or NotePad app, we will add the following lines to the top of the script - copy and paste the following to the above script:

You should have this:

STEP 6: Save the file and now let’s transfer it to the HPC. See below:

NOTE: To proceed, you need to be on QUT’s WiFi network or signed via VPN.

Windows PC: open file finder and type the address below to connect to your home directory in the HPC, and then browse to the /workshop/2024-2/session6_smallRNAseq/data/mydata folder

Mac: open file finder and press “command” + “k” to open prompt, then type the below command, and then browse to the /workshop/2024-2/session6_smallRNAseq/data/mydata folder

• Drag and drop the script into the /workshop/2024-2/session6_smallRNAseq/data/mydata folder

STEP 7: We will ensure the copied file from our laptop / desktop does not have unwanted characters. Let’s move to the data folder:

How to use the dos2unix tool? Type:

Now let’s run dos2unix conversion. Note the filename may vary, so adjust the filename as appropriate.

• Note: If you create a file using Microsoft Excel, it is likely that it will add ASCII characters, use dos2unix to remove such characters.

Now we are ready to submit to the HPC cluster the script to download FASTQ files:

Monitor progress of job:

• Note: Downloading the above datasets will take about ~50 minutes.

Find in the link below alternative approaches to download data from SRA, BaseSpace or use the nf-core/fetchngs pipeline:

Data Download