1.  Put all ACE file to be processed in the same path.  Make sure all ACE files have distinct names.
2.  Create a list(list1) of the ACE files you want to process.
3.  Run run_clean_ace.pl with list1, you should get a clean ace file directory
4.  Create a list(list2) of clean ACE files you want to further process.  You should then get a quality file directory.
5.  Run ace_fetch_qual.pl with list2.  You should get a result file directory.
6.  Make an output directory for the final step. Run run_clean_ace_snp.pl. 

You can use batch_to_unigene.pl to get unigene_id instead of assembly_ids. You will need a file with unigene_ids and assembly ids which can be produced from CGN and /or PGN wih the following query:

select unigenes.unigene_id, unigene_assembly.contig FROM unigenes JOIN unigene_assembly on (unigenes.unigene_element_id=unigene_assembly.unigene_assembly_id) WHERE unigenes.unigene_element_type_id=1 and unigene_build_id=<build_id>.


