Part 1: Use and extension of PyDegradome
Introduction Part of my PhD work consisted in studing a putative RNA endonuclease from Arabidopsis. To this end a library of mRNA degradation intermediates was prepared and sequenced (Degradome). Since tools for the analysis of such RNA species are mostly focused on the effect of miRNAs (/E.g./ Thody et al. 2018; Addo-Quaye, Miller, and Axtell 2009) a custom script developed for the analysis of targets of a viral endonuclease on human cells (PyDegradome Gaglia, Rycroft, and Glaunsinger 2015) was used. As described by the authors their approach focuses solely on the degradome samples without relying on other sequencing data such as conventional RNAseq however, in doing so, the analysis and interpretation of the results is somehow complicated. Additionally, the output of the script (consisting of a table of genomic coordinates with significant differences between two samples) requires further processing. An attempt to tackle these two tasks was done in my work and it is briefly described below.
