EU-seq and ChIP-seq data analysis upon degradation of the RNA-binding protein EIF4A3 in mouse embryonic stem cells

Bioinformatic analysis of transcriptional changes upon degradation of the RNA-binding protein EIF4A3 in mESCs. This script performs an analysis on the effects of EIF4A3 knockdown in mouse embryonic stem cells (mESCs) as part of a bachelor's thesis. It identifies on which specific genes the influence of EIF4A3 is noticeable in terms of transcription rate (analysing EU-seq data (5-ethynyl-uridine-sequencing)) and whether these genes are indicated to associate with super-enhancers (analysing the proximity) and transcriptional-Polymerase-2-clusters (examining ChIP-seq (Chromatin Immuno-Precipitation DNA-Sequencing) data). Furthermore, the script creates lists containing genomic coordinates of genes indicating to being regulated in association with transcriptional clusters. These genomic regions can then be chosen as targets of DNA Fluorescence In Situ Hybridization