[mira_talk] Re: Total consensus length is double ?
- From: Jan van Haarst <jan@xxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 13 Jul 2010 11:59:39 +0200
Dear Bastien,
Aargh !
Thanks for spotting that one !
I'll rerun the assembly with the right dataset (SRR000868-SRR000873
+ SRR001355), and if it looks good, I'll put the results up on my wiki at
https://wiki.nbic.nl/index.php/Raw_results_of_NGS_de_novo_assembly .
I guess this is the result of the fact that SRA id's do not map directly to
SRR id's.
My apologies for wasting your time, but at least MIRA let me find my error
:-)
With kind regards,
Jan
On Mon, Jul 12, 2010 at 21:38, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On Montag 12 Juli 2010 Bastien Chevreux wrote:
> > On Montag 12 Juli 2010 Jan van Haarst wrote:
> > > I have converted the datasets to SFF using sff-dump from NCBI.
> > > Like this :
> > > sff-dump -A SRR001028 -D ena/SRR001028/
> > > That is using the sff-dump that is in
> > >
> http://www.ncbi.nlm.nih.gov/Traces/sra/static/sra_toolkit-1.0.0-b7-glibc.
> > >6- x86_64.tar.gz
>
> Please forget everything I just wrote. While being true, there's something
> else first: did you really mean SRR001028? This is a human sample!
>
> SRA001028 with the attached SRR001355 would be the the way to go, wouldn't
> it?
>
> Bastien
>
> PS: and then the whole thing with the 2 files and paired-end applies only
> partly.
>
>
--
Dag,
Jan
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