Hi, I dealing right now with some ChIP-seq data generated from a very low number of cells. Data look so far good but I noticed that some loci got heavily amplified during library preparations which is I guess a consequence of working with low amounts of material. I looking now for a tool to restrict the number of identical reads per loci at for example 3 (e.g. if I have 10 identical reads 7 will be removed and 3 remain). As far as I read both picard tools as well as samtools remove duplicates in a all or nothing manner. Somebody has a handy solution for me (Iam biologist :p).