[mira_talk] Re: virus genome assembly
- From: Chris Hoefler <hoeflerb@xxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 22 May 2014 11:06:53 -0500
> and the problem is to detect RNA splicing between 2 conditions.
> I don't know if it is possible to do that with Mira.
Yes it is. But without a clear description of what your data is, where it
came from (I'm assuming cDNA library?), and other information (like do you
have a reference genome), it will be difficult to help you.
On Thu, May 22, 2014 at 10:51 AM, Chris Hoefler <hoeflerb@xxxxxxxxx> wrote:
> 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
>>>
>>>
>>>
>>> --
>>> You have received this mail because you are subscribed to the mira_talk
>>> mailing list. For information on how to subscribe or unsubscribe, please
>>> visit http://www.chevreux.org/mira_mailinglists.html
>>>
>>
>>
>>
>>
>
>
> --
> Chris Hoefler, PhD
> Postdoctoral Research Associate
> Straight Lab
> Texas A&M University
> 2128 TAMU
> College Station, TX 77843-2128
>
--
Chris Hoefler, PhD
Postdoctoral Research Associate
Straight Lab
Texas A&M University
2128 TAMU
College Station, TX 77843-2128
Other related posts:
