I am trying to assemble pacbio reads from RS II. But, the problem is that
1) we have pooled 6 BAC clones per cell but we have not barcoded the Samples. So, my first question is that can these reads be assembled.
2) The second problem with same data is we pooled the clones thinking that inserts may be overlapping sequences which seems to be true has resulted which resulted some regions overlapping high very high coverage and some regions at end and non overlapping having low coverage. Does anybody know how to tackle this problem.