[mira_talk] Re: Getting 454 test data
- From: "Khan, Anar" <Anar.Khan@xxxxxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 15 Jul 2009 09:08:35 +1200
Hi
I had a similar issue a couple of weeks ago. I wrote to the SRA Help desk and
they tracked down the specific sff files I was after. They were really helpful
(:
Click on the 'Write to the Help Desk' link on this page:
http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=main&m=main&s=main
Cheers
Anar
> -----Original Message-----
> From: mira_talk-bounce@xxxxxxxxxxxxx [mailto:mira_talk-
> bounce@xxxxxxxxxxxxx] On Behalf Of Bastien Chevreux
> Sent: Wednesday, 15 July 2009 7:13 a.m.
> To: mira_talk@xxxxxxxxxxxxx
> Subject: [mira_talk] Re: Getting 454 test data
>
> On Dienstag 14 Juli 2009 Einar Arnason wrote:
> > I'm a newbie on this list and am having trouble trying to download
> the 454
> > test data on Brucella ceti referred to in the manual:
> >
> > "Please browse to
> >
> http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?run=SRR005481&cmd=viewer
> &m=d
> >ata&s=viewer
> >
> <http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?run=SRR005481&cmd=viewe
> r&m=
> >data&s=viewer%20>and
> >
> http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?run=SRR005482&cmd=viewer
> &m=d
> >ata&s=viewerand download the SFF files to the origdata directory
> (press the
> > download button on those pages)."
> >
> > Wherever I look I cannot find the sff files (I only see possibilities
> for
> > downloading fasta or fastq). Can someone please direct me (I'm using
> > Firefox 3.5b4).
>
> Hello Einar,
>
> oh, no more SFFs from the NCBI? That's a pity. I had such an extensive
> walkthrough :-(
>
> NCBI had a few problems in the past weeks with the data they had in the
> download sections. E.g., paired-end reads from 454 were not splitted in
> forward and reverse reads etc.pp
>
> I mailed them shortly before the ISMB in STockholm and then again a few
> days
> ago about this ... and a few hours later all the SRA FTP directories
> were
> empty ... but are now getting slowly filled again. It looks like they
> are
> currently recomputing major parts of the data.
>
> Which is good, because one example I looked at (Ecoli MG1655 in
> SRX000348) now
> has splitted 454 paired-end as fastq (which wasn't the case a few days
> ago,
> even if the 'last modified' date of the FTP server suggests otherwise
> :-)
>
> Anyway, for you this currently means that you cannot follow the
> walkthrough as
> given. I will need to write an additional one which shows how to use
> the FASTQ
> from NCBI (since last week MIRA can now also load fastq) ... I hope I
> can
> manage to do that for the next release (perhaps this week-end).
>
> Sorry I can't help you out more on that at the moment.
>
> Regards,
> Bastien
>
>
>
> --
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> please visit http://www.chevreux.org/mira_mailinglists.html
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