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Update README.md
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srobb1 authored Oct 21, 2019
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12 changes: 6 additions & 6 deletions workshops/Protein_Function_Annotation/README.md
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Expand Up @@ -72,18 +72,18 @@ Currently, there are three options for service types (--service or -s).

These files (in JSON format) are in the params/ folder. They should be edited according to the uploaded data and the type of call.

**enrich.json
**This file should be used when _enrich_ is specified as the service type. There are four items to be specified in this file.
**enrich.json**
**This file should be used when _enrich_ is specified as the service type. There are four items to be specified in this file.**
1. "organism": "**9606**", _--specify an organism with a taxon ID. (see Appendix on How to find a taxon ID?)
2. "annotDataSet": "**GO:0008150**", _--specify an annotation data set. (see Appendix on How to find the ID for supported annotation dataset?)
3. "enrichmentTestType": "**FISHER**", _--enter either FISHER (for Fisher's Exact test) or BINOMIAL (for binomial distribution test)
4. "correction": "**FDR**" _--specify the multi test correction method (FDR, BONFERRONI, or NONE)

**geneinfo.json
** This file should be used when _geneinfo_ is specified as the service type. The organism taxon ID needs to be specified to match the uploaded data.
**geneinfo.json**
**This file should be used when _geneinfo_ is specified as the service type. The organism taxon ID needs to be specified to match the uploaded data.**

**ortholog.json
** This file should be used when _ortholog_ is specified as the service type. There are two items to be specified
**ortholog.json**
**This file should be used when _ortholog_ is specified as the service type. There are two items to be specified**
1. "organism": "**9606**", _-- specify the organism of the uploaded genes
2. "orthologType": "**LDO**" _-- specify the type of ortholog, e.g., LDO (for least divergent ortholog), or all.

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