[mira_talk] Problem with assembly ( some part of a contig is in reverse direction and rest is in forward direction)
- From: jyotsna guleria <jyotsna.guleria@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 23 May 2011 14:01:37 -0400
Hello All,
My parameters are:
mira --project=reads --job=denovo,genome,accurate,454 454_SETTINGS
-LR:mxti=yes -AS:mrpc=1 -OUT:stsip=yes:sssip=yes COMMON_SETTINGS
-SK:mnr=yes:nrr=10 -highlyrepetitive -CO:asir=yes
I got contig sequence in 5'-3' and 3'-5. I mean some portion of contig is
flipped, I want to verify is this a mira error or my sequence is like that?
Did any one ever got any problem like that before?
Is there any parameter that can tell mira to assemble in only one direction?
I know mira output contigs in both directions. I mean if I have got 10
contigs, I can have 6 contigs in forwrad direction and 4 in reverse
direction which is fine but I saw my sequence to be flipped in one contig (
need to check rest as well ).
Please help, this is a very important thing to verify or to be fixed if this
is an assembly error.
Many thanks !!
Jyo
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