[mira_talk] Re: Mira3 server
- From: Juan Daniel Montenegro Cabrera <jdmontenegroc@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 25 May 2011 01:11:38 -0500
Well, thank you all for your help. I found out the problem and it turned
out to be an over coverage of the sequence (near 450X), so I used the
package "Flower" and produced a new sff file with random 10 percent of the
reads. Converted them into fasta, qual and xml and re-run mira on my on
laptop. By the way, I had never used the Flower package but it seems to be
very helpful when handling 454 data, just needs to be a little more
friendly.
just in case any of you is interested in it, here is the old link:
http://blog.malde.org/index.php/2009/07/03/a-set-of-tools-for-working-with-454-sequences/
<http://blog.malde.org/index.php/2009/07/03/a-set-of-tools-for-working-with-454-sequences/>or
the new one:
http://biohaskell.org/Applications/Flower
<http://biohaskell.org/Applications/Flower>Thanks again for all your help.
Yours sincerely,
Juan Montenegro
Applied Biotechnology Laboratory
International Potato Center - Lima - Peru
2011/5/24 John Nash <john.he.nash@xxxxxxxxx>
> Seriously, isnt it about the libraries, and method of package installation?
> Other than that, I don't see much difference.
>
> As a bioinformatian, depending on what the admin has provided, I've gone
> from IRIX to SunOS to Solaris to Red Hat (to Fedora) to SUSE to Ubuntu, and
> apart from a few libraries and learning rpms and apt-get, etc, it's been
> pretty transparent. Plus I have played with a dozen or so distros for
> curiosity's sake. The transition from C to Perl was more dramatic.
>
> Sent from my mobile device
>
> On 2011-05-24, at 5:13 PM, Adrian Pelin <apelin20@xxxxxxxxx> wrote:
>
> What the problem with ubuntu?
>
> On Tue, May 24, 2011 at 4:22 PM, George Marselis
> <<George.MARSELIS@xxxxxxxxxxxx>
> George.MARSELIS@xxxxxxxxxxxx> wrote:
>
>> Friends don't let friends use ubuntu.
>>
>> ----
>> George Marselis, systems administrator
>> Building #2, Level 4, room 4327
>> Computational Bioscience Research Center, KAUST
>> Land: +966-2-808-2944, Mobile: +966-56-321-7713, Skype: project2501a
>>
>>
>>
>>
>>
>>
>>
>> On 24/5/11 7:04 PM, "Davide Sassera" < <davide.sassera@xxxxxxxx>
>> davide.sassera@xxxxxxxx> wrote:
>>
>> >With an assembly like that I think you could just do it on a good
>> >desktop computer with ubuntu installed.
>> >
>> >I'm not sure about latest mira version, but I suppose 4GB of ram would
>> >do the trick.
>> >
>> >Am I too optimistic?
>> >
>> >Davide
>> >
>> >
>> >
>> >> Dear all,
>> >> I recently tried to assemble a 454 sequencing project. I have ~190
>> >> 000 reads of 236 bp average length. Although is not a highly
>> >> demanding assembly, the server i am using crashes all the time. It is
>> >> pretty old and has a lot of users. Do you know of any other free
>> >> server i could use to run the assembly?
>> >> Still I will try to reduce the number of reads since i believe it is
>> >> over-covered.
>> >> Any ideas, i would appreciate all the help possible.
>> >>
>> >> Juan Montenegro
>> >
>> >
>> >--
>> >Davide Sassera
>> >Sezione di Patologia Generale e Parassitologia
>> >Dipartimento di Patologia Animale,
>> >Igiene e Sanità Pubblica Veterinaria
>> >Facoltà di Veterinaria
>> >Università degli Studi di Milano
>> >Via Celoria 10, 20133, Milano, ITALY
>> >Tel: +39 0250318094
>> >Fax: +39 0250318095
>> >
>> >
>> >--
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