[mira_talk] Re: Reference vs. De novo assembly.
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 21 Dec 2009 12:34:41 +0100
On Mittwoch 16 Dezember 2009 Andrzej N wrote:
> [...]
As I said: for whatever reason, chloroplast and mitochondrial
sequencing/assembly is a pretty ungrateful thing ... the uneven coverage in
data sets I've seen so far accounts for one of them. I've seen sets with
coverage variance of a factor 5 from the average coverage.
What you should do:
- a mapping assembly against a reference and then look at the coverage. Find
out whether there are parts which are extremely overrepresented. Try top find
out whether it's normal.
- also, try a de-novo assembly with adding "-AS:ard=no" and see whether this
helps. The totally uneven coverage probably fools the repeat detection.
Regards,
Bastien
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