Extraction and annotation of SAGE tags using sequence quality values.
Data analysis of serial analysis of gene expression (SAGE) tag experiments begins with the extraction of tags from single-pass sequence files of ditag concatemers. When using DNA base quality values generated during base calling, it is possible to control the false-positive discovery rate of unique tags. This chapter describes how to set up a system for generating tag lists from quality associated sequence data.
Emmersen
Jeppe
J
Department of Biochemistry, Chemistry and Environmental Engineering, University of Aalborg, Aalborg, Denmark.
D000818:Animals; D002874:Chromosome Mapping; D004247:DNA / Q000235:genetics / Q000302:isolation & purification; D015252:Deoxyribonucleases, Type II Site-Specific; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling / Q000379:methods* / Q000706:statistics & numerical data; D015723:Gene Library; D006801:Humans; D012333:RNA, Messenger / Q000235:genetics; D012984:Software
D012333:RNA, Messenger; D004247:DNA; C049760:endodeoxyribonuclease MmeI; D015252:Deoxyribonucleases, Type II Site-Specific