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Old 04-21-2009, 06:48 AM   #1
kentnf
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Default A qusetion about denovo assembly 454 sequence using MIRA

Hi,

I use mira to do assembling on my 454 sequence, but the problem is if there are two differnet nt in the same position, the contig sequence will be change.

for example:
contig1: AAAARTTTYTCCCCGGGG
member1: AAAAGTTTCTCCCCGGGG
member2: AAAAATTTTTCCCCGGGG

it means
AG =R
CT =Y
AC=M

How can change the R Y M to ATCG?

Thank you.
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Old 04-21-2009, 08:25 AM   #2
coldturkey
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I suggest joining the mira_talk mailing list http://www.chevreux.org/mira_mailinglists.html
You'll get a prompt answer to your question
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Old 04-21-2009, 10:04 AM   #3
kentnf
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hehe, Thank you!
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Old 04-21-2009, 10:37 PM   #4
sklages
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You might want to have a look at:

force_nonIUPACconsensus_perseqtype(fnicpst)=on|yes|1, off|no|0

cheers,
Sven
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Old 04-22-2009, 08:02 AM   #5
kentnf
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Thank you so much! sklages
It work when I set the -job:sanger, but not work well when set -job:454.

The new problems is how to set the ends clip in MIRA,
I try -CL:emlc and -CL:emrc, some of my sequences have different in the ends, but it not work
example is in cap3, I can set -y 15, and if the ends different lower than 15bp , it clipped.
In MIRA, it can not assembly when set -CL:emlc=no,emrc=no
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Old 04-22-2009, 09:56 AM   #6
sklages
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well, it should work with -job:454 as the manual doesn't distinguish
sequencing chemistries at this point.
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Old 04-23-2009, 10:10 AM   #7
kentnf
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Quote:
Originally Posted by sklages View Post
well, it should work with -job:454 as the manual doesn't distinguish
sequencing chemistries at this point.
I use 2.9.37 version before, maybe some other parameter different when I set -job:454 or sanger, now I download 2.9.44 version, use -CLec=yes to clip the ends of sequence, but the clipping part is too long, I want set the clipping length lower than 15bp; if clip longer than 15bp,I think the two reads can not assembly. How to set it? Thank you.
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Old 04-24-2009, 05:36 AM   #8
kentnf
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up up up up up
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