[mira_talk] MIRA assembly - Geneious 8 - extra IUPAC codes
- From: Zain A Alvi <zain.alvi@xxxxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Mon, 22 Dec 2014 12:49:27 +0000
Hi Everyone,
I was able to run MIRA this past weekend on the workstation (Geneious) with no
problems. Thank you everyone for the help.
There is one small problem that I am having is with the output. The output is
very specific and includes R, Y, S, K, and other IUPAC codes for the nucleotide
sequences. I was wondering if there is a method to make MIRA to not include
ambiguities in the alignment results. I hope to run a BLASTX based on the
genome assembly from MIRA. These IUPAC codes makes BLASTX think that I am
working with an amino acid sequences instead of nucleotide sequence.
Also does MIRA like interleaved/interlaced files for paired end alignment or
the paired end reads to be just separate like with some other assemblers like
IUPAC codes
R A or G
Y C or T
S G or C
W A or T
K G or T
M A or C
B C or G or T
D A or G or T
H A or C or T
V A or C or G
Thank you in advance.
Kind regards,
Zain
________________________________________
From: mira_talk-bounce@xxxxxxxxxxxxx <mira_talk-bounce@xxxxxxxxxxxxx> on behalf
of Zain A Alvi <zain.alvi@xxxxxxxxxxxxxxx>
Sent: Wednesday, December 17, 2014 10:36 AM
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Re: MIRA Failure - Geneious 8 - Bug report
Hi Bastien,
The error came in small dialog box, which copy pasted/exported into a text
file. I was testing MIRA via Geneious 8 on Intel i5 (4 core) computer with 10
GB of ram allocated to Geneious. I will try it again today with the BioLinux 8
Workstation. Hopefully it is just a memory problem.
Kind regards,
Zain
________________________________________
From: mira_talk-bounce@xxxxxxxxxxxxx <mira_talk-bounce@xxxxxxxxxxxxx> on behalf
of Bastien Chevreux <bach@xxxxxxxxxxxx>
Sent: Wednesday, December 17, 2014 9:27 AM
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Re: MIRA Failure - Geneious 8 - Bug report
On 17 Dec 2014, at 14:50 , Zain A Alvi <zain.alvi@xxxxxxxxxxxxxxx> wrote:
> I am using MIRA 4.0 on Geneious 8. Do you think it is Geneious error?
Not a Geneious error. Although the log file is pretty much mangled up and
incomplete (what on earth did you do with it?), I think it’s a memory problem.
> Do you think my mentor's workstation will be able to handle this?
> 128 GB of RAM
Yes.
B.
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