Advances in Next Generation Sequencing decidedly has given a momentum to molecular biology and genetics. It has been a tool for modernization of conventional techniques. A sequencing-based method ChIP-Seq is used for identification of binding patterns of DNA-associated proteins. Success of this method depends on alignment of short reads onto a reference genome. Most mappable short reads align to a single genomic location with at least the rate of %75. However existence of reads which are mapped to more than one location (multiple mapped reads) onto genome is problematic. These reads are generally excluded during studies. Various algorithms and probabilistic techniques has been developed to utilize multiple mapped reads so achieving meaningful information from these excluded reads become more possible. Due to the shortness of ChIP-Seq reads and repetitive nature of genomic DNA, a standard for aligment of multiple mapped reads has not been fully achieved yet. As of today, most ChIP-Seq studies discards multiple mapped reads.
In this study we implemented a novel approach to rescue multiple mapped reads by extending reads by library preparation length and then mapping to genome. We observed that the coverage of extended alignment overlapped with mappable or unique regions of genome. Hence, our findings reveal potential significance that multiple mapped reads carry valuable information that should be recovered and included in ChIP-Seq analysis