We have stopped to generating fastq files from mirrored NCBI/ENA SRA data to save storage spaces since 11th December 2019. We have generated and will generate fastq files of DRA data.
- NCBI SRA: sra file only
- ENA SRA: sra and fastq files
- DDBJ SRA: Before 10th December 2019, sra and fastq files. After 11th December 2019, fastq of DRA only.
| Archive | sra files | NCBI SRA fastq | ENA SRA fastq | DDBJ SRA fastq |
|---|---|---|---|---|
| NCBI SRA | O | X | X | X |
| ENA SRA | O | O | O | O |
| DDBJ SRA | O | X (since 2019-12-10) | X (since 2019-12-10) | O |
For NCBI/ENA SRA data whose fastq files are not generated, you may obtain the fastq as follows.
Download from ENA
If ENA has generated fastq of the Run of your interest (for example, ERR3350433), you may download the fastq from ENA.
Generating fastq from DRA mirrored sra file
Search the Run in DDBJ Search.
Example; ERR3350433
sra filepath;
- https://ddbj.nig.ac.jp/public/ddbj_database/dra/sralite/ByExp/litesra/ERX/ERX337/ERX3374941/ERR3350433/ERR3350433.sra
- ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/ERX/ERX337/ERX3374941/ERR3350433/ERR3350433.sra
Please see How to use prefetch and fasterq-dump to extract FASTQ-files from SRA-accessions regarding how to generate fastq from sra.