hi , currently i am doing NGS anaysis , and i have done chip seq analysis . not only till peak finding but beond that. finding motif , and locating peak in genes, wether peak is in upstream of tss , or in genic or intergenic region. we have a pipeline set for the anaysis.
so if you are really intrested in some NGS analysis beyond conventional tool runing , adding more statistics and analysis of your data let me know.
for my capabilities please visti pubmed and look for vineet jha.
Thanks