Difference between revisions of "Phenotype2GO pipeline SOP"
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| − | + | =====Phenotype2GO pipeline (Sanger and Caltech)===== | |
| − | + | *The old Sanger script that generates the gene_association file (from Igor's work in January 2009) was changed. Instead of an exclusion list and 'include list' that comprises papers (mostly large scale genome-wide studies) is provided to the script. This list is curator approved and explicitly agreed upon for the propagation of GO terms to genes based on their RNAi phenotypes. | |
| − | + | *A new script is used, to use it invoke the script with the -includelist option, e.g.: Run parse_go_terms_new.pl -o gene_association.wb -rnai -include includelist.txt (this example only parses RNAi experiments, to generate full file, you should also give '-gene -var' options as before). | |
| − | + | *If you invoke it with '-acefile <filename>' option, the script will also generate Gene-GO_term connections derived from phenotypes. This is currently done by the phenotype procedure of the inherit_GO_terms.pl script. | |
| − | + | *The old script: inherit_GO_terms.pl does not consult any exclusion/inclusion files. | |
| − | + | *To alter Sanger's version of parse_go_terms_new.pl, a patch file was provided. | |
| − | + | *Current status:From Igor's e-mail, March 2009: I don't think the phenotype option of the inherit_go_terms script has been disabled. The script should be run without the '-variation' option, but the gene_association file still has those. Try this: | |
| − | + | grep -i wbpheno gene_association.WS200.wb.ce |grep -v RNAi | |
| − | + | This is now resolved. | |
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| − | This | ||
| − | + | ==Phenotype2GO mappings== | |
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| − | + | [[Category:Curation]] | |
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Latest revision as of 04:28, 8 September 2010
Phenotype2GO pipeline (Sanger and Caltech)
- The old Sanger script that generates the gene_association file (from Igor's work in January 2009) was changed. Instead of an exclusion list and 'include list' that comprises papers (mostly large scale genome-wide studies) is provided to the script. This list is curator approved and explicitly agreed upon for the propagation of GO terms to genes based on their RNAi phenotypes.
- A new script is used, to use it invoke the script with the -includelist option, e.g.: Run parse_go_terms_new.pl -o gene_association.wb -rnai -include includelist.txt (this example only parses RNAi experiments, to generate full file, you should also give '-gene -var' options as before).
- If you invoke it with '-acefile <filename>' option, the script will also generate Gene-GO_term connections derived from phenotypes. This is currently done by the phenotype procedure of the inherit_GO_terms.pl script.
- The old script: inherit_GO_terms.pl does not consult any exclusion/inclusion files.
- To alter Sanger's version of parse_go_terms_new.pl, a patch file was provided.
- Current status:From Igor's e-mail, March 2009: I don't think the phenotype option of the inherit_go_terms script has been disabled. The script should be run without the '-variation' option, but the gene_association file still has those. Try this:
grep -i wbpheno gene_association.WS200.wb.ce |grep -v RNAi This is now resolved.
