Example workflow of data search
We strongly recommend users to start with searching articles related to data that you want. It is obvious that published article contains lot more information than metadata submitted to SRA with sequencing data.
workflow
Search research articles
- on PubMed or the other literature databases
- search articles on DBCLS SRA Publication search
- faceted search by study type, platform, and/or species
- search SRAID on articles by disease information on DBCLS SRA
Find SRA ID
- Authors often describe SRA ID on the section of materials & methods
- search "SRA/ERA/DRA" on an article page
Search by SRA ID
- See "ID based search" on Tips: data search
Select data to download
- by browsing metadata on DRASearch/ENA data browser
- detailed information about sequencing is often described in materials&methods section rather than metadata
Check and download sequencing information
- We recommend to check sequencing quality before download at DBCLS SRA Metadata toolkit to avoid downloading failed/non-suitable data
- download metadata as a text on ENA data browser, See Metadata based search
Download data
- For most Japanese institutes, FTP transfer from DRA would be the fastest.
- If the data will be used just for further analysis(no need to convert to raw data), download fastq format
Analysis
- As you like
- Using galaxy: send SRA data directly to galaxy from ENA data browser. See Analysis pipeline
If the condition of data that is going to be found was clear, using faceted search interface can be the solution. EBI Advanced Search, DDBJ DRASearch, and DBCLS SRA provide search interface that user can specify the profile of sequence data along the metadata format.
See Metadata based search and getting SRA ID, then follow the workflow above.