Adjust clipping for GAP4. The clipping reported by Phrap reflect this. GAP4 requires more stringent clipping. Automatically remove cloning vector. Completely vector reads are removed, and partial ones are clipped and tagged.
Unexpected matches are indicative of plate contamination or clone mix-ups.
Finally, a GAP4 database is created directly from the CAF file using caf2gap. Editing All editing is now performed in GAP4. Because we are sequencing overlapping clones chosen from a physical map, some redundancy of sequencing is unavoidable. To minimise the finishing and editing effort, we only finish the overlap in one of each pair of overlapping clones. In general, we start at the left end of a clone and finish to 100 bp beyond the start of the overlapping clone to the right.