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 -- 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