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.
best
miroslav
Answers and/or pointers to resources appropriate for novices would be gratefully appreciated.
best
miroslav
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