[Bioc-sig-seq] SRAdb and getFastq

[Jack Zhu]

Hi Kirti,


As Martin said, in the newer version of BioC (both 2.7 release and 2.8
dev version), there were changes to reflect the NCBI removal of fastq
files:

   1. Removed functions of listFastq, getFastqInfo and getFaastq
   2. Added functions of listSRAfile, getSRAinfo and getSRAfile
   3. Modified the corresponding files to reflect the change.

Now you could just list or get lite.sra files or sra files instead of
fastq files.  Details please see:

    https://stat.ethz.ch/pipermail/bioc-devel/2011-January/002439.html

Or the package vignette:
http://www.bioconductor.org/help/bioc-views/release/bioc/html/SRAdb.html

Regarding converting  lite.sra files into fastq files, after the sra
toolkit was installed properly, we just simple run:

 $   fastq-dump xxxx.lite.sra

FYI.

Thanks.

Jack




On 4 March 2011 15:16, kirti prakash <kirtiprakash3.14 at gmail.com> wrote:
> 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 at gmail.com> wrote:
>>
>> 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
>
>