Data search

ID based search

If you already have SRA ID of the data you want to download, there's no worry about data search. Put them into the search box and get what you want.

NCBI

GUI:

Search with SRA ID on top page, then click size of Run to open FTP, or install Aspera connect and get the data through faster transfer protocol.

via command line:

1. open ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads
2. choose and move to one of 4 directories: "ByExp", "ByRun", "BySample", and "ByStudy"
3. choose and move to "litesra" or "sra"
4. choose and go through the directories by ID prefix (e.g. SRR/SRR000/SRR000001 for SRR000001)

example:

• ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX000/SRX000001/SRR000021/SRR000021.sra
• ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/litesra/SRX/SRX000/SRX000001/SRR000021/SRR000021.sra
• ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR000/SRR000001/SRR000001.sra
• ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/litesra/SRR/SRR000/SRR000001/SRR000001.sra
• ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/BySample/sra/SRS/SRS000/SRS000002/SRR000066/SRR000066.sra
• ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/BySample/litesra/SRS/SRS000/SRS000002/SRR000066/SRR000066.sra
• ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP000/SRP000001/SRR000001/SRR000001.sra
• ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/litesra/SRP/SRP000/SRP000001/SRR000001/SRR000001.sra

EBI

GUI:

Search with SRA ID on "Text search" at top page, then choose Run and click link in the table to open FTP, or Aspera connect.

download Metdata text

On "project" browsing mode, metadata text information can be downloaded. Click "Select columns" above the table, choose information needed, then click "download TEXT" on the right side.

via command line:

1. open ftp://ftp.sra.ebi.ac.uk/vol1/fastq
2. choose and go through the directories by prefix of Run ID (e.g. ERR000/ERR000001 for ERR000001)

example:

• ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR000/ERR000001/ERR000001.fastq.gz
• ftp://ftp.sra.ebi.ac.uk/vol1/sff/ERR002/ERR002800/ERR002800.sff
  • sff file can be downloaded, if available

DDBJ

GUI:

Search with SRA ID on "Accession" at DRASearch, then choose Run and click link on the right side to open FTP

via command line:

1. open ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra
2. choose and move to fastq or sralite
3. For fastq: go through the directories by Submission ID and Experiment ID (e.g. DRA000/DRA000001/DRX000001 for DRR000001)
4. For sralite: move to ByExp/litesra and go through the directories by Experiment ID (e.g. ByExp/litesra/DRX/DRX000/DRX000001/DRR000001 for DRR000001)

example:

• ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/DRA000/DRA000001/DRX000001/DRR000001.fastq.bz2
• ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/DRX/DRX000/DRX000001/DRR000001/DRR000001.sra

Metadata based search

We recommend to search on EBI advanced search or DRASearch.

EBI Advanced Search

1. go to EBI advanced search
2. choose "Read"
3. select search condition
4. click "search" above

DRASearch

1. go to DRASearch
2. Search with keyword, using facet, or select from rankings
3. click "search"

Extra search features

DBCLS SRA provides several search features to improve accessibility to SRA data by integrating external information.

Search by statistics

From the top page of DBCLS SRA: search by statistics and one-of-a-kind faceted search. Users can start searching by clicking a name on a rankings. Weekly updated.

Search by publication

Publication search enables users to find SRA ID by publication information. Faceted search also implemented, weekly updated. Paring information between SRA ID and PubMed ID is gathered automatically - If any missing pair was found, contact us.

Search by disease information

Search by disease

Search by disease tree

Publication information we collecting also enables search by disease information. This feature is based on MeSH term information tagged in PubMed abstract information. Frequency search and tree view are provided.