Protočna struktura za detekciju grupa modificiranih nukleotida u očitanjima RNA dobivenih metodom nanopora

undergraduate thesis

• Title (english): Pipeline for Detection Clusters of Modified Nucleotides in Nanopore Sequenced RNA Reads
• Author: Ivona Martinović
• Mentor: Mile Šikić (mentor)
• Committee member: Mile Šikić (predsjednik povjerenstva)
• Committee member: Krešimir Križanović (član povjerenstva)
• Committee member: Josip Marić (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2020-07-06, Croatia
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Computing

Abstract

Glavna zadaća ovog rada je detekcija grupa modificiranih nukletida u očitanjima RNA dobivenih metodom nanopora. Podaci za ovaj rad su očitanja i referenca ribozima tetrahimena, skupine I introna iz Tetrahymena. Cilj je bio integirati postojeće alate kao što su Graphmap, Minimap i Minimap2, Ram, i Racon te ih povezati python skriptama u protočnu strukturu. Kako bi se to napravilo, svi alati za poravnavanje bili su testirani. Drugačiji pristup je takod̄er proban, poravnavanje očitanja u domeni signala. Protočna struktura sastoji se od tri dijela: odabira očitanja, poliranja i detekcije grupa modificiranih nukleotida. Izvorni kod dostupan je na: https:
//github.com/lbcb-edu/BSc-thesis-19-20/tree/imartinovic.

Abstract (english)

The main concern of this thesis is the clustering of modified nucleotides in nanopore sequenced RNA reads. The data for this thesis are reads and the reference from the tetrahymena ribozyme, a group I intron from Tetrahymena. The goal was to integrate existing tools such as Graphmap, Minimap and Minimap2, Ram, and Racon and link them with python scripts into a pipeline. To do this, all of the alignment tools were tested. A different approach for alignment was also tried out, aligning the reads in the signal domain. The pipeline was implemented in three parts: read selection, polishing and clustering of modified nucleotides. Source code is available at: https:
//github.com/lbcb-edu/BSc-thesis-19-20/tree/imartinovic.

• Keywords: RNA; protočna struktura; nanopore; modifikacije; sklearn; poravnavanje
• Keywords (english): RNA; pipeline; nanopores; modifications; sklearn; alignment
• Language: english
• URN:NBN: urn:nbn:hr:168:617498
• Study programme: Title: Computing; Study programme type: university; Study level: undergraduate; Academic / professional title: sveučilišni/a prvostupnik/ prvostupnica (baccalaureus/baccalaurea) inženjer/inženjerka računarstva (sveučilišni/a prvostupnik/ prvostupnica (baccalaureus/baccalaurea) inženjer/inženjerka računarstva)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Closed access
• Created on: 2023-01-14 09:28:38