Download Reference microRNA sequences from miRBase
First, let’s create a folder to store the reference datasets:
mkdir -p $HOME/workshop/2024-2/session6_smallRNAseq/data/references
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:
wget https://mirbase.org/download/mature.fa
Fetch hairpin sequences:
wget https://mirbase.org/download/hairpin.fa
Fetch the genomic coordinated for precursors and mature sequences:
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