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Old 12-10-2010, 09:57 AM   #31
JueFish
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Location: Connecticut

Join Date: May 2010
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Thanks again for your thoughts, Phillip. I've been doing some comparisons between different assemblies using different approaches and it seems that using the 454 kit may be preferable to the normalization approach. With all the sequencing issues associated with it, the increase handling, and longer protocol, I'm not sure the normalization is worth it. It might save us a little cash in the long run, but the incovenience and troubleshooting might just wash all that away. From comparing, assemblies (albeit from different species/tissues), it appears the quality of data that we get from the 454 kit is much better than the normalization approach, subsequent contigs appear longer, and there's less opportunity for stuff to go wrong. You do lose something in coverage, but it's not terrible if you input with something that's ribo-depleted or poly-A selected. And, since sequence length is so important in de novo assembly, it seems trying to maximize that might be our best approach to getting a good reference assembly. Anyway, that's my current two cents, if anyone is interested.
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