[mira_talk] Re: Questions from one of my researchers
- From: George Marselis <George.MARSELIS@xxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Tue, 26 Apr 2011 13:30:01 +0300
Thanks for the answers, Bastien!
Best,
----
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 23/4/11 6:50 PM, "Bastien Chevreux" <bach@xxxxxxxxxxxx> wrote:
>On Apr 21, 2011, at 18:07 , George Marselis wrote:
>
>One of my researchers has a couple of questions. I am pasting verbatim:
>1. Is there a parallel version that can use multiple nodes on a cluster to
>distribute the analysis?
>
>
>
>
>Sorry, no.
>
>
>2. How can we feed in large amount of Paired Ended data with different
>insert sizes (e.g. 16 libraries with different inserts and some with
>multiple PE sets; altogether 76 fastq files; around 200GB size on disk) +
>50 GB long reads).
>
>
>
>
>Forget it, MIRA will not work with that amount of data.
>
>
>3. Can we feed to mira pre-assembled contigs e.g. from soapdenovo along
>with the original PE libraries so that contigs can be extended; there
>seems to be a limit of 2k reads currently acceptable to mira.
>
>
>
>
>The limit is more at something like 15 to 20 kbp. Longer than that, you
>need to fragment.
>
>
>4. Is this known bug in mira solved? mapping of paired-end reads with one
>read being in non-repetitive area and the other in a repeat is not as
>effective as it should be (taken from
>http://mira-assembler.sourceforge.net/docs/chap_solexa_part.html#sect_sxa_
>k
>nown_bugs___problems)
>
>
>
>
>No, still there. On my TODO, though I do not know when I will have time
>to look at it.
>
>
>I think the answer to the first question is "no, launch multiple instances
>instead".
>
>
>
>
>Indeed, but only possible for EST assemblies which were pre-clustered.
>For genome assemblies it makes less sense as everything somehow connects
>to everything else.
>
>B.
>
>
>
--
You have received this mail because you are subscribed to the mira_talk mailing
list. For information on how to subscribe or unsubscribe, please visit
http://www.chevreux.org/mira_mailinglists.html
Other related posts:
