[mira_talk] Re: Reassembly contigs in MIRA

  • From: Andrej Benjak <abenjak@xxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Fri, 04 Jul 2014 08:41:55 +0200

Hi,
The log says that the fasta file cannot be found, so are you sure the path is correct?
But this doesn't matter really, the problem is you are feeding MIRA with assembled contigs as they were Illumina reads. They are not Illumina anymore, you assembled them with Velvet. You can assemble these contigs with MIRA using 'technology=text' or 'sanger' sure, but then it would be in your interest to delete the results right away...
Reassembling contigs can only produce unreliable results (unless you are after some special cases and you know what you are doing, I suppose). If anything gets assembled, it's likely to be misassembled. This is because contigs don't cary any information about coverage, repeats, errors etc..
So I really recommend to use MIRA on raw Illumina reads and that's it. You can always compare the results from MIRA with those from Velvet, see where the differences are etc... 

Cheers,
Andrej


On 07/04/2014 05:57 AM, suganthi appalasamy wrote:

Hi,
*I have assembled my transcriptome **r**eads with Velvet (Oases). i have few libraries of assembled contigs which i wish to reassemble all of them using MIRA. Can this be done? * 
*
*
*i tried and i found this error message in my log. *
Looking for files named in data ...Data '/media/data2/dell2/home/su/bin/Project__C1B1/Sample_lane3/C1B1_VELVET/_77/transcript_77.fa' was not found (neithe$ Data '/media/data2/dell2/home/su/bin/Project_C1B1/Sample_lane3/C1B1_VELVET/_79/trancript_79.fa' was not found (neither as file nor as directory) or led to a read error 

Fatal error (may be due to problems of the input data or parameters):

********************************************************************************
* Some 'data' entries named in the manifest file could not be verified, see * 
* the log above.                       *
* Maybe some files are missing, not readable or there is a typo in the * 
* manifest file?                       *
********************************************************************************
->Thrown: void Manifest::loadManifestFile(string & mfilename)




*My manifest.conf looks like this*


projectname = C1B1
job = genome,denovo,accurate
parameters = -GE:not=4 \ COMMON_SETTINGS -NW:cmrnl=no \ -OUT:ora=on -OUT:rtd=no -OUT:rrot=no \ SOLEXA_SETTINGS -CL:pec=on 
readgroup = unpaireddata
data = /media/data2/dell2/home/su/bin/Project_C1B1/Sample_lane3/C1B1_VELVET/_77/transcript_77.fa /media/data2/dell2/home/su/bin/Project_C1B1/Sample_lane3/C1B1_VELVET/_79/transcript_79.fa 
technology = solexa
template_size = 100 100000 autorefine



*Thank you!!*

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