Files/directories in this directory:
- annotation_H3K4me3_downstream contains the annotation generated by PITA with the parameters to look at H3K4me3 from the start site of a gene to 2000 bp downstream.
- annotation_noH3K4me3 contains the generated annotation without taking H3K4me3 into account.
- annotation_wH3K4me3 contains the generated annotation taking H3K4me3 into account with parameters 1000 bp upstream to 1000 bp downstream.
- annotation_lowH3K4me3 contains the generated annotation taking H3K4me3 into account with parameters 1000 bp upstream to 1000 bp downstream. 
	The weight is however lower than in the rest of the generated annotations: it is about half as much.

General remark on files inside these directories:
The final bed file that can be used in any of the directories is called "sorted_pita_annotation.bed". 
	The file has been sorted by chromosome, and any gene consisting of a single exon has been taken out.
	In all of these files, chromosome Dpe05 is completely missing.