Alat za mapiranje dugih očitanja dobivenih RNA sekvenciranjem

master's thesis

• Title (english): Long read RNA-seq mapper
• Author: Josip Marić
• Mentor: Mile Šikić (mentor)
• Committee member: Mile Šikić (predsjednik povjerenstva)
• Committee member: Damir Seršić (član povjerenstva)
• Committee member: Mladen Vučić (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2015-07-03, Croatia
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Computing

Abstract

RNA sekvenciranje je tehnologija koja koristi alate za sekvenciranje druge generacije za analizu transkriptoma. Bioinformatički alati se koriste za analizu RNA sljedova u svrhu otkrivanja prisutnosti i kvantitete RNA molekula u danom trenutku, što je važno za otkrivanje funkcionalnih elemenata genoma i razumijevanja razvoja bolesti. U ovom radu iznešen je alat koji je izgrađen iz metode poravnanja koju koristi BBMap alat. Razvijeni alat koristi se za poravnavanje dugih očitanja sa velikim brojem pograšaka na referentni genom. Poboljšanja razvijene metode su također iznijeta i evaluirana. Rezultati analizirani i uspoređeni sa BBMap metodom. Ovaj rad objašnjava metodu poravnavanja koju koristi BBMap i pokazuje da ista može biti reproducirana na način da proizvodi visoko precizne rezultate poravnanja RNA očitanja.

Abstract (english)

RNA sequencing is a technology that uses next generation sequencing tools for transriptome analysis. Bioinformatics tools are used to analyze RNA sequences to reveal a snapshot of RNA presence and quantity from a genome at a given time, which is important for interpreting the functional elements of the genome and understanding development of diseases. This thesis presents a tool built from the BBMap aligning method that is used in mapping long reads with high error rate to the reference genome. Improvements of the developed method are also presented and evaluated. Results are analyzes and compared to the BBMap tool. This paper explains the aligning method used by BBMap and shows that it can be recreated in such manner that it produces highly precise alignment results.

• Keywords: RNA; BBMap; poravnanje; pokrivenost; sekvencioniranje; izrezana očitanja; ekgzon; intron; indeksiranje genoma
• Keywords (english): RNA; BBMap; alignment; coverage; sequencing; spliced reads; exon; intron; genome indexing
• Language: english
• URN:NBN: urn:nbn:hr:168:998368
• 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: 2018-02-06 10:25:13