# Absolute occupancy analysis code

Please find the most up to date version and more information on GitHub:

https://github.com/gerland-group/absolute-occupancy-analysis

This archive also contains the dyad positions called by different groups (see main text) and the resulting N+1 positions,
as well as TSS and TTS positions all in the external_data folder.

Reference genomes of S. Cerevisiae and S. Pombe and spike-ins are in the reference_genomes folder.

## General

Analysis functions for N+1 alignment, comparisons of different samples, dyad occupancy calculation 
and export to bedgraph files can be found in shared_functions.R

## Restriction Enzymes / Bisulfite / EM-seq

Analyses for restriction enzyme (RE) and bisulfite (BS) start with already mapped bam files (see methods section in paper) and use 
the corresponding analysis R scripts running in numbered project folders (with additional project folders for analysing spike-in regions in the case of BS).

## Nanopore

Nanopore analyses start with the fast5 raw data files and the basecalled fastq files needed to run minimap2 and then Nanopolish 
in the script nanopore/NP1/process_barcoded_reads.sh. 

