[mira_talk] Questions from one of my researchers
- From: George Marselis <George.MARSELIS@xxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 21 Apr 2011 19:07:49 +0300
Hey guys,
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?
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).
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.
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)
I think the answer to the first question is "no, launch multiple instances
instead".
Looking forward to hearing from you,
----
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
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