From 1502ebb609e5ee69949c882b194fbb0bf9624fac Mon Sep 17 00:00:00 2001 From: rlibouban Date: Fri, 17 Apr 2026 11:38:23 +0200 Subject: [PATCH] minor changes --- .../tutorials/proteogenomics-dbcreation/tutorial.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.md b/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.md index efd429b0b331a6..79c665d0fd0767 100644 --- a/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.md +++ b/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.md @@ -98,9 +98,9 @@ In this tutorial, protein and the total RNA sample was obtained from the early d > > {% snippet faqs/galaxy/datasets_change_datatype.md datatype="fastqsanger" %} > -> 5. Make sure the Database/Build (dbkey) is set to `Mouse.Dec 2011 (GRCm38/mm10)(mm10)` +> 5. Make sure the Database/Build (dbkey) is set to `Mouse Dec. 2011 (GRCm38/mm10)(mm10)` > -> {% snippet faqs/galaxy/datasets_change_dbkey.md dbkey="Mouse.Dec 2011 (GRCm38/mm10)(mm10)"%} +> {% snippet faqs/galaxy/datasets_change_dbkey.md dbkey="Mouse Dec. 2011 (GRCm38/mm10)(mm10)"%} > > 6. **Note**: If you are running the workflow taken from the **GTN**, then make sure the tool "**Tabular-to-FASTA**" (tool number 26) > has Title Column labeled as "1" and Sequence Column as "2". @@ -233,7 +233,7 @@ data manager to create these annotations to make them available for users. > > 1. {% tool [CustomProDB](toolshed.g2.bx.psu.edu/repos/galaxyp/custom_pro_db/custom_pro_db/1.22.0) %} with the following parameters: > - *"Will you select a genome annotation from your history or use a built-in annotation?"*: `Use built in genome annotation` -> - *"Using reference genome"*: `Ensemble 89 mmusculus (GRm38.p5) (dbsnp142)` +> - *"Using reference genome"*: `Mouse (Ensemble 89 mmusculus) (mm10/GRm38.p5)` > - {% icon param-file %} *"BAM file"*: `HISAT_Output.BAM` > - {% icon param-file %} *"VCF file"*: `Freebayes.vcf` > - *"Create a variant FASTA for short insertions and deletions"*: `Yes` @@ -320,7 +320,7 @@ The original form of this program is also distributed as part of the Cufflinks s > compare assembled transcripts against a reference annotation > -> 1. {% tool [GffCompare](toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.12.6+galaxy0) %} with the following parameters: +> 1. {% tool [GffCompare](toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.12.10+galaxy0) %} with the following parameters: > - {% icon param-file %} *"GTF inputs for comparison"*`Stringtie_output.gtf` > - *"Use Reference Annotation"*: `yes` > - *"Choose the source for the reference annotation"*: `History`