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/ ).
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#!/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).
Manuscript: https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004188
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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.
Hit: it will take a couple of clicks to open multiple pages to find the identifier for the data deposited in ENA.
Which is the Array express identifier noted in the above manuscript and which ENA identifiers it relates to?
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Array Express: E-MTAB-2206 , and ENA identifier: ERP004592 |
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’:
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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 5: Open the downloaded ena file using TextEdit (NotePad or similar app). The downloaded script looks like this:
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wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/044/SRR20630344/SRR20630344.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/049/SRR20630349/SRR20630349.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/055/SRR20630355/SRR20630355.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/047/SRR20630347/SRR20630347.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/050/SRR20630350/SRR20630350.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/042/SRR20630342/SRR20630342.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/053/SRR20630353/SRR20630353.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/043/SRR20630343/SRR20630343.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/039/SRR20630339/SRR20630339.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/056/SRR20630356/SRR20630356.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/054/SRR20630354/SRR20630354.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/041/SRR20630341/SRR20630341.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/045/SRR20630345/SRR20630345.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/051/SRR20630351/SRR20630351.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/040/SRR20630340/SRR20630340.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/048/SRR20630348/SRR20630348.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/052/SRR20630352/SRR20630352.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/046/SRR20630346/SRR20630346.fastq.gz |
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:
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#!/bin/bash -l #PBS -N ENA_data_download #PBS -l select=1:ncpus=2:mem=4gb #PBS -l walltime=24:00:00 #work on current directory (folder) cd $PBS_O_WORKDIR |
You should have this:
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#!/bin/bash -l
#PBS -N nfrnaseq_test
#PBS -l select=1:ncpus=2:mem=4gb
#PBS -l walltime=24:00:00
#work on current directory (folder)
cd $PBS_O_WORKDIR
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/044/SRR20630344/SRR20630344.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/049/SRR20630349/SRR20630349.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/055/SRR20630355/SRR20630355.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/047/SRR20630347/SRR20630347.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/050/SRR20630350/SRR20630350.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/042/SRR20630342/SRR20630342.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/053/SRR20630353/SRR20630353.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/043/SRR20630343/SRR20630343.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/039/SRR20630339/SRR20630339.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/056/SRR20630356/SRR20630356.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/054/SRR20630354/SRR20630354.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/041/SRR20630341/SRR20630341.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/045/SRR20630345/SRR20630345.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/051/SRR20630351/SRR20630351.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/040/SRR20630340/SRR20630340.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/048/SRR20630348/SRR20630348.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/052/SRR20630352/SRR20630352.fastq.gz
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/046/SRR20630346/SRR20630346.fastq.gz |
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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\\hpc-fs\home\ |
Mac: open file finder and press “command” + “k” to open prompt, then type the below command, and then browse to the /workshop/2024-2/session4_RNAseq/data/mydata folder
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smb://hpc-fs/home/ |
Drag and drop the script into the /workshop/2024-2/session4_RNAseq/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:
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cd $HOME/workshop/2024-2/session4_RNAseq/data/mydata |
How to use the dos2unix tool? Type:
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dos2unix --help |
Now let’s run dos2unix conversion. Note the filename may vary, so adjust the filename as appropriate.
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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
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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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qsub ena-file-download-selected-files-20241013-1123.pbs |
Monitor progress of job:
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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:
For this approach you will need to have a list of SRA identifiers. For example, for the human Huntington Disease study the list of identifiers are:
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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
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#!/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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