[mira_talk] Re: MIRA vs Newbler (454 est's)
- From: Diogo Santos <diogofcul@xxxxxxxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Mon, 25 Jul 2011 16:39:34 +0000
Hello
I had already preprocese my data. I have extract the files from .sff with the
script extract_sff (I chosse the min_left_clip enougth to dont raise any
warnig). After that I use seqclean and only after that I run mira with
-job=denovo,accurate,est,454 , i turn of the polyA processing because seqclean
already do it...
Best regardsDiogo Santos
From: gierski@xxxxxxxxxxxxxxxxxx
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Re: MIRA vs Newbler (454 est's)
Date: Mon, 25 Jul 2011 17:29:42 +0200
Hello,
Start with reading a MIRA manual:
http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html
Part about 454 sequences is important:
http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#chap_454
Usually you need to preproces data.
After that you call mira with: mira -project=NAME_OF_PROJECT
-job=accurate,denovo,genome,454
--
With best regards, Przemyslaw Gierski.
From:
mira_talk-bounce@xxxxxxxxxxxxx [mailto:mira_talk-bounce@xxxxxxxxxxxxx] On
Behalf Of Diogo Santos
Sent: Montag, 25. Juli 2011
17:19
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] MIRA
vs Newbler (454 est's)
Hello
I have received data from an EST's project from 454. they
make the assembly with Newbler 2.5 and they get 5869 contigs (length>100)
with coverage 11x (I know it's low, but it's what I get:( ). I try to use MIRA
to make some testing and use the original data to reassemble, but I get a
strange result (19378 contigs with length >100 and coverage 4x). Can you teel
wich parameters should I change?
Thanks
Diogo
Santos
Other related posts:
