Hybrid_project

1. To convert the gff file of S. uvarum (available at http://www.saccharomycessensustricto.org/cgi-bin/s3.cgi?data=Annotations&version=current) run the commands in GFF_GTF_conversion.txt

2. To obtain the orthologuos promoter regions in of S. cerecisiae and S. uvarum, for each species first run the script create_promoters.py. Example:

python create_promoters.py Saccharomyces_cerevisiae.R64-1-1.93.gtf Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa SC_promoters_1000bp.fasta > SC_promoters_1000bp.bed

3. Then run the script create_orthologous_promoters.py using the bed files created by the previous script.

4. To obtain the possibly regulated closest genes to ATACseq peaks, run the commands finding_cis_genes.txt