This repository contains scripts and plots analyzing the Stentor genome.
Contents:
- RNAseq_preprocessing.sh - script for trimming and filtering fastq files prior to mapping
- RNAseq_mapping.sh - script for mapping to genome with Bowtie2
- plotReadCounts.R - R script for visualizing reads mapped per contig
- readsmapped.png - plots showing reads mapped per contig for our RNAseq data, with (1) raw counts and (2) counts normalized by contig length
- compareReplicateLibraries.R - R script for plotting read counts from 2 replicate libraries to assess their similarity
- rnaseq_coverage_1.png - plot showing RNAseq coverage across 10kb of contig 1. Plus strand coverage in red, minus strand coverage in blue.