Doubts in Agilent Sure select DNA design

Question

[Amk]

Hi,

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

Amk

[Benn]

Shouldn't you ask Agilent about this?

[Amk]

Hi b.nota,

You know any technical team in Agilent to talk about this?

[Benn]

Agilent is a big company, it shouldn't be difficult to contact the customer service. Maybe check their website for their technical assistance team.

Answer 1

[User 59]

1) The design will not perform 100% as expected, therefore you will expect some differences between its theoretical and real-world performance. This is entirely normal.

2) I'm pretty sure Agilent don't give away probe sequences any more with the design. Every design 'target' will have many probes mapping to it, Agilent generally overlap probes in their designs.

3) Probably someone doing 0 and 1 based counting? ;) I don't know. It sounds a bit unusual that there would be a numeric relationship like this between regions which are designed to and regions which aren't?

And the commenter is right, contact Agilent Tech Support: https://earray.chem.agilent.com/suredesign/help/Contact_Agilent_Technical_Support.htm