Using long- and short-read RNA-seq to study minor class intron splicing
This repository contains code used to perform the analysis and generate the figures for my PhD thesis chapter 4.
Files and folders
aligned_minimap2: genomic alignment BAM files and scripts for mapping
bambu: scripts and outputs for bambu
salmon: scripts and outputs for salmon
short_bam_merged: merge bams of samples from the same group for visualization of coverage
transcript_analysis: scripts and outputs for transcriptomic analysis: quality control, DTE, DTU, visualization of read coverage
DTE and DTU results table
These can be found in transcript_analysis/results (for long read) and transcript_analysis/results_short (for short read).