Scripts to find putative introgressions using wheat axiom array data
Download this script (script.pl) and identify_introgressions.pl and put in the same directory as the data files: sample_type.txt, map_info.txt and genotyping_data.txt. These are all available as a zip file at http://www.cerealsdb.uk.net/introgression_data.tar.gz as they are too large to host here
Check that script.pl and identify_introgressions.pl are both executable and that the directory has RW permissions then run with: nohup ./script.pl &
Once the job is complete, the output files can be processed with the use of the pipeline.pl script, with the shell script process_files.pl feeding all of the directories created by script.pl into the pipeline one at a time:
nohup ./process_files.pl &
This will create a directory called OUTPUT with a summary file for each potential introgression donor with the introgression scores for each wheat variety in columns and the axiom marker in rows.