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Two contigs, one very short

Posted: Thu Feb 11, 2010 4:08 pm
by jstamm
I have a number of projects (DMAC-12a and DMAC-33b, for example) where I have a single large contig and then one small contig with only a few reads in it. This small contig contains fewer than 1000 bp. Also, at least for DMAC-12a, there appear to be tandem repeats in the 2 contigs, so that it would likely be very difficult to sequence across the gap.

Can we just assume that since the fosmid clones overlap substantially, we don't have to worry about the ends, or should we try to close the gap?