Quality of Base Calling for NextGeneration Sequence

• Main Authors: Yi-ChunLin, 林怡君
• Other Authors: Shih-Huang Chan
• Format: Others
• Language: en_US
• Published: 2015
• Online Access: http://ndltd.ncl.edu.tw/handle/62028518932776264013

碩士 === 國立成功大學 === 統計學系 === 103 === There are four different bases, adenine (A), guanine (G), cytosine (C), and thymine (T), making up DNA. Next Generation Sequencing is a new technique allowing to sequence DNA much more quickly and cheaply than the previously used Sanger sequencing. However, issue on quality of sequencing, although plays an important role in coding the DNA, does not receive much attention academically and practically. Illumina, one of the famous companies, claims that the positions of bases follow the same sequels vertically after the fourth cycle. However, several works have been conducted and proved that the positions of base calling are not fixed. See Li (2012), Shao (2013) and Lin (2014). The above authors basically used a specific region to prove that there does exist a shift in base position. In the thesis, we apply machine learning technique called eigenface recognition and principal component scores to represent the overall behavior of cycles, and find the relationship between shift and cycles using the coefficients of eigenfaces.