DNAmethylation is an important biological process involving in human disease such as cancer Insomia and Diabetes. Bisulfite sequencing (BS-Seq) with nextgeneration technology is an accurate method for measuring DNA methylation. BSseq data analysis is a considerable way to recognize methylated cytosines and several tools have been developed to analysis BS-Seq such as BS-Seeker, BSOLANA, BRAT, BSMAP and etc. In this paper, we propose a novel idea to get more efficiency in the sequencing process, This idea will improve the rate of accuracy in the BSOLANA alignment tool using a new method in the preprocessing step. Our method is based on modification in some regions of DNA strand named CpG islands. CpG islands are significant regions in DNA strand which frequency of methylated cytosines is less than other CpG contexts. We compared our method with previous methods in the preprocessing of the original BSOLANA tool using on HG19 reads. The comparison shows that new method provides more ability to align read sequences in the BSOLANA.
