Why is the number of cDNA library less than the number of molecules?

[GoogleCodeExporter]

When I did not check the options "Fragmentation" and "cutoff" on the panel
Library, the number of molecules is same as the number of cDNA(reads). But
when I checked the options "Fragmentation" and "cutoff" on the panel
Library, the number of cDNA(reads) is less than the number of molecules,
the factor is about 10%. Based on my understanding, the number of
cDNA(reads) should be more than the number of molecules.

I read the following answer to the question, but the reason why estimated
factor is 0.562 have not been explained clearly. 
http://fluxcapacitor.wikidot.com/forum/t-168375/how-can-i-create-a-certain-numbe
r-of-reads

I guess it is related to the protocol, but I am not sure what the default
protocol is in the Flux Simulator.

Thanks

Original issue reported on code.google.com by Guorong...@gmail.com on 18 May 2010 at 4:49

[GoogleCodeExporter]

Hi,

this is more a discussion topic than an Issue, I moved it to the Flux Forum:

http://fluxcapacitor.wikidot.com/forum/t-242498/why-is-the-number-of-cdna-librar
y-less-than-the-number-of-molecules#post-788219

You can comment there, therefore I close the issue here.

Original comment by gmicha@gmail.com on 19 May 2010 at 12:24

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