We have been using Agilent Sureselect DNA for targeted sequencing of a particular gene. We came across some doubts. It would be helpful if someone could help out.
1. The percent coverage shown in the report is not matching with calculated percetage coverage from the bed file using "Missed" and "Covered" Regions. Why? (We calculated the percentage coverage by adding up the covered and missed regions length individually from bed file, We could not see any overlaps in the covered or missed regions in bed file.)
2. The total probes mentioned in the report file was significantly more compared to bed file covered region number. Is bed file actually showing number of probes or simply covered regions?
3. In bed file (All_Tracks) the covered and missed regions is always like missed = covered - 1. (Eg : If 793 is covered then 792 will be the missed ones) Why is it so?
Thanks in advance.