[mira_talk] vector clipping

Hi all,

I have one project involving BACs sequencing on 454 Titanium. I tried to
clip vector using ssaha:

ssaha cra_in.454.fasta vector.fasta -d0 -pf
     >cra_ssahavectorscreen_in.txt

and then invoking mira:

mira -projectin=cra -projectout=cra_v2
     -job=denovo,genome,454,accurate
     COMMON_SETTINGS -GE:not=8
     454_SETTINGS -CL:msvs=1

but projects ends with the "megahubs" message and shows 5% of reads to
be in megahubs, which is roughly vector portion. Indeed from the
cra_v2_int_clippings.0.txt file it looks that vector is not clipped
away. File name of the ssaha output seems to be ok (it is the same name
as expected by mira written in the mira log).

Am I missing some parameter? Do anyone have some hint?

Thank you for your help,

Jan Paces

Institute of Molecular Genetics
Czech Academy of Sciences
Czech Republic


-- 
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: