engleski

Pipeline for Detection Clusters of Modified Nucleotides in Nanopore Sequenced RNA Reads

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.

RNA ; pipeline ; nanopores ; modifications ; sklearn ; alignment

nije evidentirano