what are thoughts on this new method? no need for a covaris, and low input. interested in using before capture protocol, i am concerned the transposome complex will not yield fragments representative of entire genome.
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what are thoughts on this new method? no need for a covaris, and low input. interested in using before capture protocol, i am concerned the transposome complex will not yield fragments representative of entire genome. -
Moving this to the library prep forum as it's applicable to 454 (and probably solid) as well. -
size distribution using transposition
I heard about the new technology as well. I was just wondering what the size distribution looks like afterwards. As far as I know there is no need to do it. Thanks.Comment
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here is the distribution with bioanalyzer for a full reaction with 10 pcr cycles:
and for 1/5 scaled down reaction with 15 pcr cycles:
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here is the distribution with bioanalyzer for a full reaction with 10 pcr cycles:
[IMG]
[/IMG]
and for 1/5 scaled down reaction with 15 pcr cycles:
http://www.postimage.org/image.php?v=PqE_Lh9[IMG]
[/IMG]
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You should check with your capture reagent vendor -- one of the problems seen with Illumina libraries is "daisy-chaining" of fragments via the adapters which brings in off-target material. Nextera uses custom adapters, so any blocking oligos supplied in the kit won't be correct.Comment
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@upenn_ngs: Were this size distributions for Illumina libraries?Comment
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what about ends fragments ?
Hi all,
This fragmentation seems very interesting by its low input DNA and its relative simplicity!
I am wondering about the non representativity of ends fragments with this fragmentation except with a previous step like circularization or adding primers.
Is that makes sense ?
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yes, this is illumina library prep. although there is a great time saving, a fragmentation and ligation protocol with NEB enzyme is still much more cost effective.Comment
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