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LOcating Non-Unique matched Tags(LONUT) -improving the detection of the enriched regions for ChIP-seq and MBD-seq data

Wang, Yisong
http://rave.ohiolink.edu/etdc/view?acc_num=osu1306170566

Abstract Details

2011, Master of Science, Ohio State University, Computer Science and Engineering.
In this thesis, a computational approach (LONUT) aiming to locate non-unique matched tags to genome is implemented in Perl Language and UNIX system. In addition, LONUT has been applied on several public datasets as well as those from my lab’s collaborators to investigate biological consequences. LONUT utilizes several existing bioinformatics Tools besides its own scripts. The first tool it employs is a tag alignment Tool Bowtie, an ultrafast memory-efficient short tag aligner. This thesis uses Bowtie to find possible locations of non-unique matched tags. The second Tool LONUT uses is Repbase, which is a database concluding all the coordinates of Repeats regions. LONUT makes use of it to classify whether non-unique matched tags belong to any Repeats region. The third Tool LONUT employs is a peak calling program named by BELT, which was development in my lab and a Tool BALM used to estimate genome-wide methylation level (CpG methylation) using MIRA-seq.
Victor Jin, PhD (Advisor)
Yusu Wang, PhD (Committee Member)
Computer Science
computer science

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Citations

  • Wang, Y. (2011). LOcating Non-Unique matched Tags(LONUT) -improving the detection of the enriched regions for ChIP-seq and MBD-seq data [Master's thesis, Ohio State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=osu1306170566

    APA Style (7th edition)

  • Wang, Yisong. LOcating Non-Unique matched Tags(LONUT) -improving the detection of the enriched regions for ChIP-seq and MBD-seq data. 2011. Ohio State University, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=osu1306170566.

    MLA Style (8th edition)

  • Wang, Yisong. "LOcating Non-Unique matched Tags(LONUT) -improving the detection of the enriched regions for ChIP-seq and MBD-seq data." Master's thesis, Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1306170566

    Chicago Manual of Style (17th edition)

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© 2011, all rights reserved.
This open access ETD is published by The Ohio State University and OhioLINK.