[mira_talk] pacbio reads on debrislist
- From: DUBOST AUDREY <Audrey.Dubost@xxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 19 Feb 2014 09:01:43 +0000
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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