Insert size standard deviation

[phlojo]

Hi All,

I'm working on de novo assembly using Allpaths. What's the best way of figuring out the standard deviation for the fragment and insert sizes? I've got Bioanalyzer electropherogram traces; is it sufficient to eyeball the standard deviation from that? Thanks!

[lorendarith]

Fragment size =/= insert size, especially for the small PE fragment libraries just to clear that up.

And yes, you can eyeball it from the library end product on the bioanalyzer, just be sure to substract twice the adapter length from your bioanalyzer reading and it is ok.

[pmiguel]

Assemble with a less lazy assembler that will calculate this for you. (Eg ABySS-PE). Even if you must use Allpaths, you can get the size distribution from a preliminary ABySS assembly.

You might imagine that your bioanalyzer result will tell you the right answer, but for the most part I never find that to be the case.

--
Phillip