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