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shiltemann merged 1 commit into from
Apr 20, 2026
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minor changes #6793

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8 changes: 4 additions & 4 deletions topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.md
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Expand Up @@ -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".
Expand Down Expand Up @@ -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`
Expand Down Expand Up @@ -320,7 +320,7 @@ The original form of this program is also distributed as part of the Cufflinks s

> <hands-on-title>compare assembled transcripts against a reference annotation</hands-on-title>
>
> 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`
Expand Down