Dear Bastien, Thanks for the answer. And if it is GC-rich? I am reluctant of using more than 100x, because of people here saying it is not good. Also, because MIRA gets very slow. N. > On Oct 18, 2011, at 22:06 , Nestor Zaburannyi wrote: >> Can i instruct MIRA to trash a read that it is going to map next if >> the coverage is more than n-fold in this particular place? > No. >> Can this feature be implemented easily? > Yes and no. Yes because it would be a couple of lines, very easy. > No, I won't do that because the effect would be totally different > that you would expect: it would lead to a stall of contig > construction and hence the assembly being fragment in thousands of pieces. >> The reason for this - i have a Bacteria >> with 800x coverage. When i take a reasonable subset (80x), it gets >> assembled, but not so good. I *suspect* that with such approach i can >> close many gaps with this coverage. Can MIRA community coment on this? > If this is not a GC rich bug ... already with 80x I suspect that > most things should assemble pretty well. You can give it a try at > 120x or 160x, but if that does not assemble neither, you either > - have a repeat there > - caught a case where Illumina has severe sequencing problem > - caught a case where MIRA is doing something foolish. > B. -- З повагою, Nestor mailto:nestor@xxxxxxxxxxxxx -- 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