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 readsCheck 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] *De la part de* Andrej Benjak*Envoyé :* mercredi 19 février 2014 10:22 *À :* mira_talk@xxxxxxxxxxxxx *Objet :* [mira_talk] Re: pacbio reads on debrislistI 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
