Fetching public NGS Data
Let's say you want to fetch the data from the public server (GEO) using the ID GSE52856, which is a dataset of RNA-seq data from N2a mouse cell lines treated with shRNA against the gene Ptbp1 and/or Ptbp2, and store the data in the directory /path/to/output. The command will be:
| # Docker
docker run --rm -v $(PWD):$(PWD) naotokubota/snakengs:latest \
ngsFetch -i GSE52856 -o $(PWD)/GSE52856
# Singularity
singularity exec docker://naotokubota/snakengs:latest \
ngsFetch -i GSE52856 -o ./GSE52856
|
./GSE52856 will contain the data fetched from the public server:
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22 | GSE52856/
├── fastq
│ ├── log
│ │ ├── md5sum.log
│ │ ├── SRR1043121_1.fastq.gz.log
│ │ ├── SRR1043121_2.fastq.gz.log
│ │ ├── SRR1043122_1.fastq.gz.log
│ │ ├── SRR1043122_2.fastq.gz.log
│ │ ├── SRR1107524_1.fastq.gz.log
│ │ ├── SRR1107524_2.fastq.gz.log
│ │ ├── SRR1107525_1.fastq.gz.log
│ │ └── SRR1107525_2.fastq.gz.log
│ ├── SRR1043121_1.fastq.gz
│ ├── SRR1043121_2.fastq.gz
│ ├── SRR1043122_1.fastq.gz
│ ├── SRR1043122_2.fastq.gz
│ ├── SRR1107524_1.fastq.gz
│ ├── SRR1107524_2.fastq.gz
│ ├── SRR1107525_1.fastq.gz
│ └── SRR1107525_2.fastq.gz
├── GSE52856_fastq_ftp.txt
└── GSE52856_metadata.json
|
fastq directory contains the fastq files fetched from the public server, and GSE52856_fastq_ftp.txt and GSE52856_metadata.json are the files containing the FTP links and metadata of the fetched data, respectively. md5sum.log files are the log files for the MD5 check of the fetched data. If the MD5 check succeeds, md5sum.log will contain the message below:
| ./GSE52856/fastq/SRR1043121_1.fastq.gz: OK
./GSE52856/fastq/SRR1043121_2.fastq.gz: OK
./GSE52856/fastq/SRR1043122_1.fastq.gz: OK
./GSE52856/fastq/SRR1043122_2.fastq.gz: OK
./GSE52856/fastq/SRR1107524_1.fastq.gz: OK
./GSE52856/fastq/SRR1107524_2.fastq.gz: OK
./GSE52856/fastq/SRR1107525_1.fastq.gz: OK
./GSE52856/fastq/SRR1107525_2.fastq.gz: OK
|