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Old 03-07-2017, 12:46 PM   #6
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Originally Posted by SDPA_Pet View Post
Hi Genomax,

Thanks. What you said makes me think the sequencing center send me a wrong report. They might mean the largest fragment. It doesn't make any sense for them to build so large fragment. 2X150bp only can sequence 300 bp maximum. If they build a library size of 600 bp, there are 300bp gaps out there. The coverage won't be very good.

2X150bp only can sample 300 bp from a fragment (for what ever size fragment, as long as it can get sequenced). You also need to keep in mind that there will always be a "normal" distribution of fragment sizes in your library with some tailing on both sides. How those tails look may determine the outcome of what preferentially clusters (small fragments would) on the flowcell.

Choice of insert sizes depends on what you are trying to do. 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. If you must have the entire region covered by the two reads (i.e. reads need to overlap) then you would want to make inserts smaller.

Which of these two cases were you wanting to do?
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