[mira_talk] Re: virus genome assembly

  • From: Laurent MANCHON <lmanchon@xxxxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Thu, 22 May 2014 22:12:07 +0200

Le 22/05/2014 21:40, Bastien Chevreux a écrit :

On 22 May 2014, at 21:28 , Laurent MANCHON <lmanchon@xxxxxxxxxxxxxx> wrote:

That being said, maybe your problem can be reduced a bit. You wrote detected … 
does that mean “counting” of known variants or “discovery” of new variants?

just counting


For counting of known variants, what I’d do would be a simple test by simply 
putting all splicing variants

this is here my question, how to select or isolate this bag of splicing 
variants from mira results ?

Ummm … if these are known variants you want to count, you have the sequence of 
those right? Then make a fasta file with these, map your reads against these 
(strict settings etc.), then look up in the statistics file of MIRA how many 
reads mapped. Or am I missing something here?

B.




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?

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