[mira_talk] Re: 454 mapping
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 06 May 2012 19:57:34 +0200
On 05/03/2012 01:22 PM, davis gimode wrote:
I am trying to do a mapping assembly of 454 data on to a reference
genome. My call parameters are:
mira --project=indica --job=mapping,genome,accurate,454 -AS:nop=4
-SB:load_backbone=yes:startbackboneusage_inpass=3:backbone_strainname=indica_backbone_in.fasta:backbone_filetype=fasta:bbq=-1
However, it requires quality scores for the backbone i.e it wants
indica_backbone_in.fasta.qual which i dont have. How do i disable mira
from requiring the quality files?
Well, MIRA will load a quality file if present, but won't stop (at least
it should not).
Which version of MIRA are you using? In 3.4.0, MIRA loads the FASTA,
sees that there's no quality file and just trots along. Here's the
relevant part of the log output:
------------------------ snip -----------------------------------
Localtime: Sun May 6 19:46:46 2012
Loading backbone from FASTA file: indica_backbone_in.fasta (quality:
indica_backbone_in.fasta.qual)
Could not find FASTA quality file indica_backbone_in.fasta.qual, using
default values for these reads.
Localtime: Sun May 6 19:46:46 2012
Counting sequences in FASTA file:
------------------------ snip -----------------------------------
By the way: your contains two errors and a minor problem:
1) (minor) -SB:sbuip is used only for combined mapping/de-novo
assemblies. You do not do that here, so it's useless to state it.
2) -SB:bsn is the name of your backbone organism, not the name of a
file. I.e., change
-SB:bsn=indica_backbone_in.fasta
to something like
-SB:bsn=IThinkThatStrainIsAnIndicaOrWhateverYouWantToNameThatThing
3) -SB:bbq should be set independently of read qualities. Using bbq=-1
is usefull only for very special borderline cases. Go with a quality of
"30": -SB:bbq=30
B.
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