diff --git a/topics/transcriptomics/tutorials/minerva-pathways/tutorial.md b/topics/transcriptomics/tutorials/minerva-pathways/tutorial.md index 6a25266ae5eca7..a834fce37d3809 100644 --- a/topics/transcriptomics/tutorials/minerva-pathways/tutorial.md +++ b/topics/transcriptomics/tutorials/minerva-pathways/tutorial.md @@ -242,6 +242,19 @@ MultiQC report. Looking at the report we see generally reasonable quality data. > - `Add Definition` → `List Identifier(s)` → Select Column `B` > - `Add Definition` → `URL` → Column `A` > +> > Trouble entering? +> > 1. Press the {% icon tool %} button by **Rules** +> > 1. Paste the following JSON into the dialog: +> > ```json +> > {"rules":[],"mapping":[{"type":"collection_name","columns":[2]},{"type":"list_identifiers","columns":[1],"editing":false},{"type":"url","columns":[0]}],"genome":"hg19"} +> > ``` +> > 1. Click Apply +> {: .tip} +> +> 1. At the bottom of the dialog set `Genome` to `hg19` (it is probably something like "Human Feb 2009 (GRCh37/hg19) (hg19)" but we are focused on that last parenthetical portion). +> +> 1. Click **Upload** +> {: .hands_on} @@ -250,17 +263,6 @@ Now we're ready to analyse the counts files. Here we'll take the feature counts With this result in hand we're ready to do two further steps: preparing the dataset for goseq, and for analysis in MINERVA. Goseq is a tool for gene ontology enrichment analysis, and MINERVA is a tool for visualising pathway analysis. -The MINERVA dataset must be correctly formatted as a tabular dataset (`\t` separated values) like the following: - -``` -SYMBOL logFC P.Value adj.P.Val -TRIM25 2.07376444684004 1.2610025125617e-18 3.57368112059986e-15 -ACSL1 2.90647033200259 2.71976234791064e-16 3.85390324698937e-13 -NBEAL2 2.45952426389725 2.71787290816654e-14 2.56748394058132e-11 -MIR150 -2.55304226607428 9.55912390273625e-14 6.74866152827879e-11 -SLC2A3 2.95861349227708 1.19066011437523e-13 6.74866152827879e-11 -``` -
{% assign wf_counts = site | get_workflow:page, "Galaxy-Workflow-mRNA-Seq_BY-COVID_Pipeline__Analysis.ga" %}
@@ -281,6 +283,17 @@ You should have a few outputs, namely the `goseq` outputs, and a table ready for
 
 ## MINERVA
 
+The dataset prepared for MINERVA must be correctly formatted as a tabular dataset (`\t` separated values) like the following, with the dbkey set to `hg19` or `hg38`. If you've run the above workflow, this should be the case.
+
+```
+SYMBOL  logFC              P.Value               adj.P.Val
+TRIM25  2.07376444684004   1.2610025125617e-18   3.57368112059986e-15
+ACSL1   2.90647033200259   2.71976234791064e-16  3.85390324698937e-13
+NBEAL2  2.45952426389725   2.71787290816654e-14  2.56748394058132e-11
+MIR150  -2.55304226607428  9.55912390273625e-14  6.74866152827879e-11
+SLC2A3  2.95861349227708   1.19066011437523e-13  6.74866152827879e-11
+```
+
 > Visualise in MINERVA
 >
 > 1. **Click** to expand the final "MINERVA-Ready Table"