I have assembled contigs by using valvet and got 335 contigs, then my question is : how can I get scaffold, or how can I get single contig? I tried to mapp this contigs to the reference genome but the problem was that consesus sequence produced contains a lots of unknow bases( indicated by ????????), and it is difficult to know a closer related reference?
How can I submit in Gene bank? can I submit contigs or consesus sequence , I am vey confused so much
plz help me guys