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 using SRA tools
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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cat launch_fetch_SRA.pbs |
Use singularity container:
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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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