This repository contains the code for the analysis of FUS CLIP-seq data from WT mouse brain homogenate and synaptoneurosome preparations. Each sample consists of two file for the two different smears that we see on the blot: One at 70k where FUS runs and another smear at 115k. In our analyses, we focused on the 70k samples.
The FASTQ files were processed with a modified version of the ARMOR workflow. The repository includes all code that was used to explore the data. For the final analysis, we used peaks called by CLIPper and a custom filtering based on MA plots (see Rmd/target_gene_selection_analysis.Rmd).