[mira_talk] Re: virus genome assembly
- From: Chris Hoefler <hoeflerb@xxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 22 May 2014 15:41:29 -0500
I've never used it, but UnSplicer may be of help here,
http://opal.biology.gatech.edu/paul/unsplicer/index.htm
On Thu, May 22, 2014 at 3:24 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On 22 May 2014, at 22:12 , Laurent MANCHON <lmanchon@xxxxxxxxxxxxxx>
> wrote:
> > […]
> > arghhh, not so easy,
> > i have one reference sequence (HIV genome sequence)
> > second i have 2 cDNA libraries 454: libA_treated and libB_not_treated
> > we know that we have some RNA spliced in libA
> > but we don't know how many and which.
> > The problem is to analyze this differential expression between libA and
> libB and
> > and highlight the spliced RNAs.
> > How to procced ? --> map libA on HIV genome, then map libB
> > and finally compare the two resulting sam files if you can find
> information on splicing ?
>
> Indeed … not see easy and I am out of options here. I’d probably need to
> see the data and play around with it to get a feeling of what the best
> approach could be, but … nope, I’m not gonna do that :-)
>
> B.
>
>
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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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