Dear all,

I am doing a targeted methylation analysis on circulating tumor DNA. After bisulfite conversion, I do Whole Bisulfitome Amplification, since DNA concentration after the bisulfite conversion is very low. After that, I amplify the methylation fragments by PCR. I visualize my PCR results by gel and see very clear bands of the expected size. I pool all the fragments together and use them for library preparation using NEB Ultra DNA library from NEB(https://international.neb.com/products/e7645-nebnext-ultra-ii-dna-library-prep-kit-for-illumina#Protocols,%20Manuals%20&%20Usage). After size selection, I do quality control by the bioanalyzer, I did not get my fragments. What could be the reason?

Thanks for your help!