i also have my problems with oases and it is still kind of a black box because there is no paper about it. If you want less Ns you could probably just reduce the insert length. Of course this is the tricky way and probably not that reasonable. ;-)
Let me know when you figured out how exactly oases does scaffolding. I tried to get some information out of the code, sad it is not easy to "read" .
if you have a near relative where the proteome is known you could try out this sort of scaffolding: http://genome.cshlp.org/content/20/10/1432 .
What you could try for expression level is mapping back the velvet contigs which are used for oases, since these have the coverage in there ID you will also get and idea about the expression levels.
Let me know when you figured out how exactly oases does scaffolding. I tried to get some information out of the code, sad it is not easy to "read" .
if you have a near relative where the proteome is known you could try out this sort of scaffolding: http://genome.cshlp.org/content/20/10/1432 .
What you could try for expression level is mapping back the velvet contigs which are used for oases, since these have the coverage in there ID you will also get and idea about the expression levels.
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