Hello,

I guess that `LIBRARY_NUMBER` refers to the Sequencing Section, where it is a variable in the formula rather than meant to be a variable in the `.PAR` file. Next time I am over the manual pages, I will try to choose variables in the formulas that are more clearly distinguishable from presumptive parameter names - however, I have choosen these long names as they are more intuitive.

Now to your question: the number of cDNA molecules is a complex function of the initial RNA molecules that have been expressed (i.e., parameter `NB_MOLECULES`), their lengths, and the parameters set for RT, Fragmentation and Filtering. So the most simple way to raise the number of molecules in the cDNA library is to start with a higher number of `NB_MOLECULES`. However, also keep an eye on your library construction sets - currently the parameters are not checked and you could for instance choose an interval for size selection that is completely out of range considering the fragment distribution, which consequently could reduce the number of molecules from whatever value to "0".

I have not yet tried to deduce general formulas for estimating the library size depending on `NB_MOLECULES`, it is also questionable whether such an undertaking is worth the efforts. Generally I suggest to estimate the (library size)/ `NB_MOLECULES` ratio for a desired set of library parameters with few initial `NB_MOLECULES`, and then use this factor to scale back from the desired library size to an approximate necessary value for `NB_MOLECULES`. See also How can I create a certain number of reads

Cheers