...
| Code Block |
|---|
wget https://www.mirbase.org/download_file/hairpin.fa |
Fetch the genomic coordinated for precursors and mature sequences:
| Code Block |
|---|
--mirna_gtf /work/trtp/data/mirbase/hsa.gff3 |
Alternatively, submit the following PBS Pro script to the cluster. Before running the script, create a ‘reference’ folder (i.e., /myteam/data/reference/ ).
| Code Block |
|---|
#!/bin/bash -l
#PBS -N nfsmrnaseq
#PBS -l select=1:ncpus=2:mem=4gb
#PBS -l walltime=24:00:00
cd $PBS_O_WORKDIR
wget https://www.mirbase.org/download_file/hairpin.fa
wget https://www.mirbase.org/download_file/mature.fa
wget https://www.mirbase.org/download_file/hsa.gff3/ |
Run a test
Before running the pipeline with real data, run the following test:
...
| Code Block |
|---|
#!/bin/bash -l
#PBS -N nfsmrnaseq
#PBS -l select=1:ncpus=2:mem=4gb
#PBS -l walltime=24:00:00
cd $PBS_O_WORKDIR
module load java
NXF_OPTS='-Xms1g -Xmx4g'
nextflow run nf-core/smrnaseq -r 2.1.0 \
-profile singularity \
--outdir outdir \
--input samplesheet.csv \
--genome GRCh38 \
--three_prime_adapter 'AACTGTAGGCACCATCAAT'\
--fastp_min_length 18 \
--fastp_max_length 30 \
--hairpin /work/trtp/data/mirbase/hairpin.fa \
--mature /work/trtp/data/mirbase/mature.fa \
--mirna_gtf /work/trtp/data/mirbase/hsa.gff3 |
Submit the job to the HPC cluster:
...