[mira_talk] On getting 454 data
- From: Einar Arnason <einararn@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 17 Jul 2009 13:18:12 +0000
I wanted to share with the list the reply I got from the NCBI helpdesk
regarding getting sff files for the mira 454 walk-through. They want to
make datasets available for such walk-throughs.
Regards
Einar
---------- Forwarded message ----------
From: Stine, Adam (NIH/NLM/NCBI) [C] <stineaj@xxxxxxxxxxxxxxxx>
Date: 2009/7/17
Subject: RE: [JIRA] Assigned: (TR-1864) missing sff files for SRR005481 and
SRR005482 accession numbers
To: Einar Arnason <einararn@xxxxxxxxx>
Hi Einar,
That is a well written walk-though and unfortunately we don’t have the data
readily available. I think you would be fine with a ‘dumped’ version of
those files. It will contain all the sequencing data but be lacking the
parts I mentioned in a previous email. I have emailed the programmer that
builds those tools to see if we can make those files for you.
Thank you for the link to the walkthrough. We hope to build a collections
section of our database that will make it easier to download data sets that
are being used in this way.
Adam Stine
NCBI/NLM/NIH [C]
*From:* Einar Arnason [mailto:einararn@xxxxxxxxx]
*Sent:* Thursday, July 16, 2009 4:38 PM
*To:* Stine, Adam (NIH/NLM/NCBI) [C]
*Subject:* Re: [JIRA] Assigned: (TR-1864) missing sff files for SRR005481
and SRR005482 accession numbers
Hello Adam,
I need these files to go through a mira walkthrough
http://www.chevreux.org/uploads/medi/mirav2946_454dev.html#section_21
As far as I can tell from the instructions I need the original files for
this. I appreciate if you could find those
Best regards
Einar
2009/7/16 Stine, Adam (NIH/NLM/NCBI) [C] <stineaj@xxxxxxxxxxxxxxxx>
Hello Einar,
Sff is a file type that we do not keep readily available. I have looked to
see if I could find the original uploaded files, but unfortunately they are
on tape archive and not quickly accessible. It could take some time to have
storage load the tape so that we can pull the files. We can generate new
sff files but they will lack the manifest and index that would have been at
the tail end of the originals.
Let me know if either of those options suit your needs and I will work on
getting the files.
Adam Stine
NCBI/NLM/NIH [C]
>
> E-mail: einararn@xxxxxxxxx
> Subject: missing sff files for SRR005481 and SRR005482 accession numbers
> Location:
http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=main&m=main&s=main
> Hi
> I am tryting to find and download the sff datga files for accession
numbers SRR005481 and SRR005482 . I cannot find the sff files looking for
example at
http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?run=SRR005481&cmd=viewer
> Please advice on how I can download sff files for these experiments.
> Thanks
> Einar Arnason
> User Agent='Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.1b4)
Gecko/20090427 Fedora/3.5-0.20.beta4.fc11 Firefox/3.5b4'
> IP=85.220.111.205
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--
-----------------------------------------------------
Einar Arnason, Professor einararn@xxxxx
Institute of Biology
University of Iceland
Askja # 346 office 354-525-4613
Sturlugata 7 lab 354-525-4606
101 Reykjavik fax 354-525-4069
Iceland
-----------------------------------------------------
--
-----------------------------------------------------
Einar Arnason, Professor einararn@xxxxx
Institute of Biology
University of Iceland
Askja # 346 office 354-525-4613
Sturlugata 7 lab 354-525-4606
101 Reykjavik fax 354-525-4069
Iceland
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