1. A computer-implemented method for deduplicating data, comprising: receiving at a storage system over a network from a client a data stream having a sequence of a plurality of data objects, the data stream representing a file or a directory of one or more files of a file system associated with the client, wherein the data stream includes a plurality of boundary markers inserted by the client prior to being received at the storage system; scanning the data stream to recognize a plurality of boundary markers each being associated with each of the data objects, the boundary markers identifying boundaries of the data objects; and deduplicating the data stream into a plurality of deduplicated chunks in view of boundaries of the data objects marked by the boundary markers, wherein deduplicating the data stream comprises anchoring the data stream using a predetermined chunking algorithm to create a plurality of anchor points, each anchor point identifying a chunking boundary for deduplication; relocating at least one of the anchor points to a location that is identified by at least one boundary markers; and chunking the data stream into the deduplicated chunks based on the anchor points that include at least one relocated anchor point.