Page Comparison

miRBase and MirGeneDB

Download Reference microRNA data from miRBase

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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:

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wget https://mirbase.org/download/hsa.gff3

OPTION #2: submit the following PBS Pro script to the cluster. Before running the script, create a ‘reference’ folder (i.e., /myteam/data/reference/ ).

#!/bin/bash -l
#PBS -N nfsmrnaseq
#PBS -l select=1:ncpus=2:mem=4gb
#PBS -l walltime=2:00:00

cd $PBS_O_WORKDIR

wget https://www.mirbase.org/download/hairpin.fa
wget https://www.mirbase.org/download/mature.fa
wget https://www.mirbase.org/download/hsa.gff3

Fetch public small RNA-seq data

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

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• 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.

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

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

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

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STEP3: (if applicable) select one or more BioProject submission(s). Click on the first listed BioProject ID:

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• STEP4: Select FASTQ files (tick boxes next to the file names) and click on “Get download script”. This will download a bash script (e.g.,

  View file
  name ena-file-download-selected-files-20241009-0005.sh

  )

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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/session4_RNAseq/data/mydata folder

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dos2unix -n ena-file-download-selected-files-20241013-1123.sh ena-file-download-selected-files-20241013-1123.pbs

• 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:

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Monitor progress of job:

qjobs

• 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:

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singularity run -B $PWD /work/training/tools/sif_lib/sra-tools_v2.10.7.sif \
  fastq-dump \
  --split-files \
  --outdir $HOME/workshop/2024-2/session6_smallRNAseq/data/mydata \
  --option-file sra ids.txt

deprecated

#!/bin/bash -l
#PBS -N rna
#PBS -l select=1:ncpus=1:mem=8gb
#PBS -l walltime=24:00:00

#Enable the container modules
source /pkg/shpc/enable

#Load the SRA-TOOLS module
module load sra-tools/3.0.5--h9f5acd7_1

#work on current directory (folder)
cd $PBS_O_WORKDIR
for i in $(cat SRR_Acc_List.txt);
do
  echo $i
  prefetch.3 $i
  fasterq-dump.3 --split-files $i
done
gzip *fastq

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