Hybrid_project
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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
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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
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Then run the script
create_orthologous_promoters.py
using the bed files created by the previous script. -
To obtain the possibly regulated closest genes to ATACseq peaks, run the commands finding_cis_genes.txt