From ad99a2ea713a09c584e3488389c1d57cda7091c6 Mon Sep 17 00:00:00 2001 From: Sofia Robb Date: Mon, 21 Oct 2019 19:30:38 -0400 Subject: [PATCH] Update README.md --- workshops/Protein_Function_Annotation/README.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/workshops/Protein_Function_Annotation/README.md b/workshops/Protein_Function_Annotation/README.md index 15e32e5..3341571 100644 --- a/workshops/Protein_Function_Annotation/README.md +++ b/workshops/Protein_Function_Annotation/README.md @@ -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.