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Old 11-06-2017, 07:33 AM   #2
Markiyan
Senior Member
 
Location: Cambridge

Join Date: Sep 2010
Posts: 115
Lightbulb Some insetrions are flanked with duplication or deletion events...

Quite a few insertional events (esp transposase induced are flanked by the target sequence duplication).
In other cases it can be accompanied by the region deletion/replacement, so it would have both start and stop.

PS: If you have enough reads coverage, assemble the sequences de novo and compare the region of interest in both assemblies using mummer/dotplot/(www)BLAST in master/slave mode.

Also you can use raw read(s) spanning the region of interest and map them using BLAST/BLASR or similar alignment tool which is able to handle the raw pacbio error rate...
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