We are currently having a hard time defining precisely molarities of our MNase-ChIP-seq libraries before sequencing using the rather classical combination between 2100 Bioanalyzer (for average fragment size estimation) and Qubit or qPCR (for quantification), and some of our runs failed due to lane saturation.

The problem we have is related to the fact that, in this type of libraries, the distribution of fragment size is rather broad. Due to cell number limitations and other biological considerations, we can't go through gel size selection step.

Has anyone any suggestion ?

Thans a lot.