Short Read Archive format

[dbrami]

Hi,

I have downloaded data from the SRA but can't seem to find any sort of file that I am familiar with. The bulk of the data seems to reside in binary 'data' files.
No FASTQ for Illuminas, no SFF's for 454.
Does anyone have any experience with pulling data from the SRA?

[jkbonfield]

There's an SRA toolkit somewhere at the NCBI you can download. Last time I used it I found it as clear as mud, needing an XML configuration file to drive it with no (working) examples or schema describing it. However it was also still in development so hopefully it's easier now.

The directories full of binary files though may not be what you wanted. They contain sequences, qualities, but also raw trace data. Unless you're planning on recomputing the qualities or running your own base-caller then it's likely that this was too much data.

Instead I'd suggest downloading the fastq files which are elsewhere on their ftp site. Eg:

ftp://ftp.ncbi.nlm.nih.gov/sra/static/SRX000/SRX000429/

or via the web:

http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=srr001665

[dbrami]

Thank you for showing the 'static' part of the ftp - i managed to download just the fastq's as desired...