[Bioc-sig-seq] SRAdb and getFastq

[Steve Lianoglou]

Hi,

On Fri, Mar 4, 2011 at 2:34 PM, kirti prakash
<kirtiprakash3.14 at gmail.com> wrote:
> Hi Sean and Martin,
>
> Thanks a lot for the clarification.
>
> Do you some other function now that converts SRA to fastq format ?

You can do it via the sra toolkit. Some info and download link here:

http://www.ncbi.nlm.nih.gov/books/NBK47540/

> I wonder how much space NCBI saves by deleting fastq files and what is extra
> advantage of having of SRA files.

Run the (I believe) fastq-dump tool to convert to FASTQ and see for yourself ;-)

It's weird -- I have a set of *.fastq.gz files for a set of *.sra
files, and the corresponding *.fastq.gz files seem to actually be
smaller!

Maybe it's just me, though ...

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact