[mira_talk] Vector screen
- From: hikaru <hsuenaga@xxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 14 Mar 2011 17:15:30 +0100
Hi all,
I am performing a assemble of 454 data with clipping the cloning vector
sequences using SSAHA2 or SMALT.
SSAHA2 and SMALT certainly recognized vector regions in each 454 read
sequences. The Mira assembly process was done completely without any
error. But the vector sequence were still remained in assembles; Checked
by SSAHA2 and BLAST search. The yielded contigs contain the vector
sequences at the (one or both) terminal of them and sometimes at the
middle of contigs (chimera?).
Has anyone had a similar problems? Is there a any way to correct the
problem?
[ssaha2]
ssaha2 -output ssaha2 -kmer 8 -skip 1 -seeds 1 -score 12 -cmatch 9
-ckmer 6 /path/where/the/vector/data/resides/vector.fasta
bchoc_in.sanger.fasta > <projectname>_ssaha2vectorscreen_in.txt
[SMALT 0.4.3]
smalt index -k 7 -s 1 idx vector.fasta
smalt map -f ssaha -d -1 -m 7 idx seqs.fasta > seqs.ssaha_out
[Mira 3.2.1]
mira -project=bchoc -job=denovo,genome,normal,sanger -fasta 454_SETTINGS
-CL:msvs=yes
“Done merging SSAHA2 vector screen data” was shown in log when SSAHA2
and SMALT file (<projectname>_ssaha2vectorscreen_in.txt) were used.
Thanks,
Hikaru
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