[mira_talk] Re: Getting 454 test data
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 14 Jul 2009 21:13:24 +0200
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=viewer&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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