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Old 01-09-2012, 04:01 PM   #2
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Location: Boston area

Join Date: Nov 2007
Posts: 747

Yuck! You certainly have an ugly situation.

I think if I were in your shoes I would try as many different approaches as possible to identify paired end reads where at least one of the pairs can be mapped to the region (existing assembly, mapping to your RNA-Seq data that you think is in the region, etc), then try assembling that with Velvet or another assembler. Then use that assembly to identify additional paired end reads mapping in & repeat. Keep cycling until things don't seem to be getting better.

Is there a publicly available BAC or cosmid library for zebrafish? I doubt you'll get anything like what you want without some long-range sequence information, and pulling out a big clone for the region could be a bunch of work but is one of the more obvious ways to go about it. Alternatively, have you tried making mate pair libraries for the whole genome?
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