Download Reference microRNA sequences from miRBase
First, let’s download a copy of miRBAse reference sequences, including hairpin and mature microRNA sequences.create a folder to store the reference datasets:
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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:
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wget https://mirbase.org/download/mature.fa |
Hairpin Fetch hairpin sequences:
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wget https://mirbase.org/download/hairpin.fa |
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wget https://mirbase.org/download/hsa.gff3 |
Alternatively, 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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