Detekcija grupa modificiranih nukleotida u očitanjima RNA dobivenih metodom nanopora

master's thesis

• Title (english): Detection of Modified Nucleotide Clusters in Nanopore Sequenced RNA Reads
• Author: Josipa Lipovac
• Mentor: Mile Šikić (mentor)
• Committee member: Mile Šikić (predsjednik povjerenstva)
• Committee member: Damir Seršić (član povjerenstva)
• Committee member: Krešimir Križanović (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2021-07-09, Croatia
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Computing

Abstract

Glavni cilj ovog diplomskog rada bio je detektiranje grupa modificiranih nukleotida u RNA očitanjima dobivenim sekvencerima treće generacije. Očitanja dobivena sekvencerima treće generacije često sadržavaju veliku količinu šuma. U ovom radu provedene su detaljne analize podataka kako bi se šum pokušao ukloniti te kako bi se podatci mogli bolje razumjeti. Prikazan je trenutni postignuti rad u području ovog problema. Provedeno je grupiranje raznim metodama kao što su K-means, Graph Spectral Clustering te Non-negative matrix factorization. Metode grupiranja testirane su na simuliranim skupovima podataka kao i na stvarnim skupovima podataka. Rezultati su prikazani tablično i grafički.

Abstract (english)

The main goal of this thesis was to detect groups of modified nucleotides in RNA reads obtained by third generation sequencers. Reads obtained by third-generation sequencers often contain a large amount of noise. In this work, detailed analyzes of the data were performed in order to try to remove the noise and so that the data could be better understood. The related work achieved in the area of this problem is shown. Clustering was performed by various methods such as K-means, Graph Spectral Clustering and Non-negative matrix factorization. Clustering methods were tested on simulated datasets as well as on real datasets. The results are presented in tables and graphs.

• Keywords: RNA modifikacije; metode grupiranja; analiza podataka; nanopor očitanja
• Keywords (english): RNA modifications; clustering methods; data analysis; nanopore reads
• Language: english
• URN:NBN: urn:nbn:hr:168:247595
• Study programme: Title: Computing; Study programme type: university; Study level: graduate; Academic / professional title: magistar/magistra inženjer/inženjerka računarstva (magistar/magistra inženjer/inženjerka računarstva)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Closed access
• Created on: 2023-01-13 12:54:11