Alternatively, to the above approach we can also use the nextflow nf-core/fetchngs pipeline to download data.
To run the this pipeline we need to inputs: 1) list of SRA identifiers and 2) PBS Pro script to fetch the data using sratools.
First, prepare a file with the list of SRA IDs of interest to be downloaded:
Hint:
In the terminal create a new folder called ‘fetchngs’. For example:
mkdir $HOME/workshop/2024-2/session4_RNAseq/data/fetchngs #then, move to the newly create folder cd $HOME/workshop/2024-2/session4_RNAseq/data/fetchngs
Copy the following list of IDs. Hint click on the top right corner of the block below to copy the text.
SRR20622172 SRR20622173 SRR20622177 SRR20622176 SRR20622180 SRR20622174 SRR20622178 SRR20622179 SRR20622175
Alternatively, instead of list of SSR identifiers it is possible to download all data in a given BioProject ID:
PRJNA862097
NOTE: Either the list above or citing the BioProject ID in the ‘ids.csv’ file will download exactly the same data.
Create a ‘ids.csv’. file using nano and paste the list of IDs:
nano ids.csv
Next, copy and paste the following PBS script to download the specified files in ‘ids.csv’.
NOTE: instead of listing individual SRR identifiers it is also possible to list the BioProject ID (e.g., PRJNA862107) which will fetch all SRR samples automatically.
Secondly, create a launch PBS script to download the data for the above IDs
Copy the block of code below. Hint click on the top right corner of the block below to copy the text.
#!/bin/bash -l #PBS -N nf_fetchngs #PBS -l select=1:ncpus=2:mem=4gb #PBS -l walltime=48:00:00 #work on current directory cd $PBS_O_WORKDIR #load java and set up memory settings to run nextflow module load java export NXF_OPTS='-Xms1g -Xmx4g' #run the RNAseq pipeline nextflow run nf-core/fetchngs \ -profile singularity \ --input ids.csv \ --outdir data \ --download_method sratools \ --nf_core_pipeline rnaseq \ -resume
Use nano to create a launch script, for example:
nano launch_nf_core_fetchngs.pbs
Paste the block of code above and save the file.
Submit the the download job to the HPC cluster:
qsub launch_nf_core_fetchngs.pbs
Outputs:
data
├── custom
│ └── user-settings.mkfg
├── fastq
│ ├── SRX16645917_SRR20622180.fastq.gz
│ ├── SRX16645918_SRR20622179.fastq.gz
│ ├── SRX16645919_SRR20622178.fastq.gz
│ ├── SRX16645920_SRR20622177.fastq.gz
│ ├── SRX16645921_SRR20622175.fastq.gz
│ ├── SRX16645922_SRR20622174.fastq.gz
│ ├── SRX16645923_SRR20622173.fastq.gz
│ ├── SRX16645924_SRR20622176.fastq.gz
│ └── SRX16645925_SRR20622172.fastq.gz
├── metadata
│ ├── SRR20622172.runinfo_ftp.tsv
│ ├── SRR20622173.runinfo_ftp.tsv
│ ├── SRR20622174.runinfo_ftp.tsv
│ ├── SRR20622175.runinfo_ftp.tsv
│ ├── SRR20622176.runinfo_ftp.tsv
│ ├── SRR20622177.runinfo_ftp.tsv
│ ├── SRR20622178.runinfo_ftp.tsv
│ ├── SRR20622179.runinfo_ftp.tsv
│ └── SRR20622180.runinfo_ftp.tsv
├── pipeline_info
│ ├── execution_report_2024-08-29_14-23-00.html
│ ├── execution_timeline_2024-08-29_14-23-00.html
│ ├── execution_trace_2024-08-29_14-23-00.txt
│ ├── nf_core_fetchngs_software_mqc_versions.yml
│ ├── params_2024-08-29_14-23-05.json
│ └── pipeline_dag_2024-08-29_14-23-00.html
└── samplesheet
├── id_mappings.csv
├── multiqc_config.yml
└── samplesheet.csv