[mira_talk] Re: virus genome assembly

  • From: Laurent MANCHON <lmanchon@xxxxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Thu, 22 May 2014 17:25:55 +0200

Le 22/05/2014 17:18, Chris Hoefler a écrit :
You cannot get 600 bp reads on a HiSeq, so the first thing you have to do is understand what kind of data you have. 

no no sorry, it's a mistake, it was 454 single end.
and the problem is to detect RNA splicing between 2 conditions.
I don't know if it is possible to do that with Mira.
My first idea was to use first gmap to map the reads onto genome, then run cufflinks on the resulting bam .
- What is the read length? On a HiSeq 100 bp is typical, but 150 bp is also an option. 
  - Is it paired or unpaired data?
- If it is paired data, what is the library insert size? This is probably where your 600 bp number comes from, but your sequencing provider should have measured the distribution. Mira likes to know the minimum and maximum. - If it is paired data, what is the orientation of the reads (innie or outie)? For a typical paired-end experiment it is innie.
Strictly speaking, Mira can manage without the last two, but it is best to give it as much information as you can. For the manifest file, you can grab a good starting place from the Mira4 manual, 
http://mira-assembler.sourceforge.net/docs/#sect_dn_mf_manifest_for_pairedend_data
http://mira-assembler.sourceforge.net/docs/#sect_ref_manifest_basics
On Thu, May 22, 2014 at 2:31 AM, Laurent MANCHON <lmanchon@xxxxxxxxxxxxxx <mailto:lmanchon@xxxxxxxxxxxxxx>> wrote: 

    Le 21/05/2014 23:19, Bastien Chevreux a écrit :

        On 21 May 2014, at 22:00 , Laurent MANCHON
        <lmanchon@xxxxxxxxxxxxxx <mailto:lmanchon@xxxxxxxxxxxxxx>> wrote:

            Does someone has already used MIRA to assemble a viral
            genome (HIV type) using long reads(600bp) libraries ?
            An example of manifest file would be welcome…

        Technology?



    HiSeq
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