Hi Steve,

I did try sra toolkit. In my case the difference between files is around
100mb.

I got fastq files by instructions mentioned at the following website ...
http://seqanswers.com/forums/archive/index.php/t-8220.html

Some issues I had with sra toolkit(I know this not the right place to
discuss this still ...):

FIrst I tried fastq-dump (a blank output file) and then illumina-dump which
gave me a set of
1. *.qcal.txt( which contains sequences like "hhhhhhhhhhhehhhhhThhLhhL")and
2. *.seq.txt (which contains info like "1       1       875     885
TACATGGGGAAAATATGCAAAATA")

I have yet to figure out how to convert this into fastq.

Kirti

On Fri, Mar 4, 2011 at 9:47 PM, Steve Lianoglou <
mailinglist.honeypot@gmail.com> wrote:

> Hi,
>
> On Fri, Mar 4, 2011 at 2:34 PM, kirti prakash
> <kirtiprakash3.14@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
>

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