[mira_talk] Too many rep_c?
- From: Thomas Müller <thomas.mueller@xxxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 22 Jul 2010 15:13:57 +0200
Hi,
I have two normalized cDNA libraries from the same tissue, one is the control
sample the other one was extracted after stress. I assembled both with mira
(after some nasty preprocessing) which resulted in about
40000 contigs, of which about 24000 are marked with rep_c and 16000 are marked
with _c (and some with _s) for each library.
As I don't have much experience with that I have some questions:
Is the number of rep_c I receive too high for a cDNA library? Have I made a
mistake in the mira call (see below)?
Or sounds the number of contigs and repetitive contigs ok to you? The organism
is a tree...
Is there a more direct way to get sequences which are assembled in both samples
than blasting the results against each other (for the rep_c this ends up in
plenty of hits)?
Any comment about the call is highly appreciated ;) :
mira --project=nnn -job=denovo,454,est,normal --notraceinfo -SK:not=10
-AS:urd=no -OUT:rld=yes -AS:sd=no -CO:asir=yes 454_SETTINGS -LR:mxti=no
-CL:qc=no -CL:cpat=no -AS:epoq=no -AL:mrs=90 -CO:rodirs=10 -SK:pr=80 -AS:mrl=50
-AL:mo=20 -FN:fai=nnn.fasta -FN:fqui=nnn.qual
Thanks for any help!
Cheers,
Thomas
--
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:
