[mira_talk] Re: pacbio reads on debrislist
- From: DUBOST AUDREY <Audrey.Dubost@xxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Tue, 25 Feb 2014 14:07:11 +0000
Ok I will test this 2 ways.
thanks
De : mira_talk-bounce@xxxxxxxxxxxxx [mailto:mira_talk-bounce@xxxxxxxxxxxxx] De
la part de Andrej Benjak
Envoyé : mercredi 19 février 2014 10:30
À : mira_talk@xxxxxxxxxxxxx
Objet : [mira_talk] Re: pacbio reads on debrislist
Perhaps this is the problem then. As far as I know, MIRA doesn't handle raw
PacBio reads (these contain a lot of errors, mostly indels).
There are 2 ways to error correct PacBio reads:
self correction
using external reads
Check the PacBio tutorial for how to error correct reads using the SMRT
Analysis tools.
If you have a decent coverage of raw PacBio reads (around 100 ideally) the self
correction will work great. If the coverage is not good, using Illumina reads
might help a little, but you still won't get a lot of long error corrected
reads...
(ah.. Juan, you were faster)
Andrej
On 02/19/2014 10:23 AM, DUBOST AUDREY wrote:
Just the filtered raw reads
Audrey
De : mira_talk-bounce@xxxxxxxxxxxxx<mailto:mira_talk-bounce@xxxxxxxxxxxxx>
[mailto:mira_talk-bounce@xxxxxxxxxxxxx] De la part de Andrej Benjak
Envoyé : mercredi 19 février 2014 10:22
À : mira_talk@xxxxxxxxxxxxx<mailto:mira_talk@xxxxxxxxxxxxx>
Objet : [mira_talk] Re: pacbio reads on debrislist
I am curious, are the PacBio reads error corrected or just the filtered raw
reads?
Andrej
On 02/19/2014 10:01 AM, DUBOST AUDREY wrote:
Hello,
I have a question with MIRA4.
I want to assemble pacbio reads and illumina reads.
First, I want to test only pacbio reads, all parameters are in manifest file
like this:
project = variant180214
job = genome,denovo,accurate
parameters =-NW:mrnl=0 -SK:mmhr=1 -NW:cac=no -GE:not=10 -AS:nop=1 -HS:ldn=y
-CO:mr=no\
PCBIOHQ_SETTINGS -AS:mrpc=1 -OUT:sssip=y
# defining the paired-end Illumina reads, fixing all needed pair information
# defining the pacbio reads, fixing all needed pair information
readgroup = Pacbio
data = variant_in.pacbio.fastq
technology = pcbiohq
To accelerate computation time I have taken -AS:nop to 1 , AS:mrpc=1 (because I
want to put illumina reads after this assembly)
On 200 000 pacbio reads, only 2500 are used in assembly...the rest is on
debrislist with "no_overlap" so I try with -HS:ldn=y -CO:mr=no but it change
nothing...
Do you have any idea of this problem?
Thanks in advance
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