[mira_talk] Re: virus genome assembly
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 22 May 2014 21:13:55 +0200
On 22 May 2014, at 17:25 , Laurent MANCHON <lmanchon@xxxxxxxxxxxxxx> wrote:
> 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 .
Disclaimer: my experience with viral sequences is minimal. I once played around
a little bit with public data, but that is just about all.
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?
For counting of known variants, what I’d do would be a simple test by simply
putting all splicing variants into a reference file and map your reads against
that (with relatively struct settings). Of course, reads coming from regions
which are in common with all variants will be evenly distributed, but reads
from certain splicing variants will automatically be mapped to the variant
matching the best. Then it’s just a counting problem. You can even “improve”
that detection by simply taking the splice junction +/- 30 bp as bait for
“mirabait”. If the 454 data is from late 454 machines, there is some hope that
not too many sequencing errors would be there and again you’d have a simple
counting problem.
If it’s for de-novo discovery … hmmm … maybe I’d try a mapping with strict
settings followed by a de-novo of unmapped reads. At least for Illumina that’s
work.
B.
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