[mira_talk] Re: virus genome assembly
- From: Chris Hoefler <hoeflerb@xxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 22 May 2014 10:51:47 -0500
So are you trying to assemble a genome denovo, or map reads? Mira can do
both.
On Thu, May 22, 2014 at 10:25 AM, Laurent MANCHON
<lmanchon@xxxxxxxxxxxxxx>wrote:
> 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>wrote:
>
>> Le 21/05/2014 23:19, Bastien Chevreux a écrit :
>>
>> On 21 May 2014, at 22:00 , Laurent MANCHON <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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>
>
>
>
--
Chris Hoefler, PhD
Postdoctoral Research Associate
Straight Lab
Texas A&M University
2128 TAMU
College Station, TX 77843-2128
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