[mira_talk] Re: pacbio reads on debrislist

  • From: Andrej Benjak <abenjak@xxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Wed, 19 Feb 2014 10:22:08 +0100

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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