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Old 03-07-2017, 01:41 PM   #9
SDPA_Pet
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Location: US

Join Date: Apr 2013
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Quote:
Originally Posted by GenoMax View Post
What kind of samples are these and what will you be doing with them (assembly?) downstream?
They are soil samples. I did shotgun metagenomics and I am insterested in microbial communities. I will not assemble it, because normally less than 1% of reads can be assemble. My plan is joined whatever reads can be joined and get longer reads. Then, to annotate it using the long reads. Those samples are from environments and you don't really have prior knowledge about what is in it. The workflow is different from model organism.

PS, I don't understand in your previous post about "If you have a reference available then making the libraries so the two ends do not overlap makes sense since you can sample a larger region". Just curious. I don't do model organisms and so normally there is no reference database. However, if they chose 2X150bp and have a reference database, but use 600 bp inserts. You can only sequence 150 bp from either end, but I still can't get information about 300 bp in the middle of the fragment. Why would they build a larger fragment library?
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