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Old 11-05-2012, 06:11 AM   #1
miroslav
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Default Agilent capture baits

I am setting up targeted sequencing using custom Agilent capture system. The design of the capture baits returned nearly 100,000 probes. The information is provided as BED file. Is there a good way of evaluating the design quality, other than manually inspecting location of 1000s of probes (), before committing to kit production? In particular, the coverage of different loci varies considerably - presumably on account of repeats and perhaps GC content variation (?). What are relative merits of bait boosting vs higher density tiling (1X density vs 2X density)?
Answers and/or pointers to resources appropriate for novices would be gratefully appreciated.
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Old 11-05-2012, 07:00 AM   #2
ECO
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Manually inspecting? IGV.

More automated...I use coverageBed all the time to check one region versus another.
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Old 11-16-2012, 02:34 AM   #3
miroslav
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Default capture baits

Thanks ECO for the pointers - slowly getting on top of this.
Is there any resource that could explain benefits of different options in targeted capture probe design? For instance, bait boosting (by Agilent protocol) appears to help with high GC regions and orphan probes but has no effect on target coverage. The probe density appears to have moderate effect on coverage but at a significant cost in terms of number of probes required for the same target as one would expect. I would like to learn how to balance these things but not sure where to start.
Any help would be appreciated
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