[mira_talk] Re: pacbio reads on debrislist
- From: Juan Pascual Anaya <jpascualanaya@xxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 19 Feb 2014 18:25:59 +0900
Then, you should read this first.
http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=PacBioToCA
PacBio reads must be corrected using reads from other technologies, or
self-corrected, before being able to do anything.
Cheers,
Juan
On Wed, Feb 19, 2014 at 6:23 PM, DUBOST AUDREY
<Audrey.Dubost@xxxxxxxxxxxxx>wrote:
> Just the filtered raw reads
>
> Audrey
>
>
>
> *De :* 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
> *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
>
>
>
>
>
--
Juan Pascual-Anaya, PhD
Research Scientist
Laboratory for Evolutionary Morphology
Center for Developmental Biology (CDB) RIKEN
2-2-3 Minatojima-minamimachi
Chuo-ku, Kobe, Hyogo 650-0047
Japan
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