From 6de4ca82499a8f63da2ad8753172b890fa5d0136 Mon Sep 17 00:00:00 2001 From: Tristan Reynolds <31689286+tflowers15@users.noreply.github.com> Date: Mon, 6 Jul 2026 10:19:02 +1000 Subject: [PATCH 1/3] Update tool input dataset names to match imported datasets --- .../tutorials/braker3/tutorial.md | 30 ++++++++++--------- 1 file changed, 16 insertions(+), 14 deletions(-) diff --git a/topics/genome-annotation/tutorials/braker3/tutorial.md b/topics/genome-annotation/tutorials/braker3/tutorial.md index 39c49710c534e0..d056a14c0322b3 100644 --- a/topics/genome-annotation/tutorials/braker3/tutorial.md +++ b/topics/genome-annotation/tutorials/braker3/tutorial.md @@ -36,12 +36,16 @@ contributions: authorship: - rlibouba - abretaud + editing: + - tflowers15 reviewing: - deeptivarshney - shiltemann - funding: - eurosciencegateway + - unimelb + - melbournebioinformatics + - AustralianBioCommons requirements: - type: internal @@ -85,9 +89,7 @@ To annotate our genome using Braker3, we will use the following files: > > {% snippet faqs/galaxy/histories_create_new.md %} > -> 2. Import the files from [Zenodo]({{ page.zenodo_link }}) or from -> the shared data library (`GTN - Material` -> `{{ page.topic_name }}` -> -> `{{ page.title }}`): +> 2. Import the files from [Zenodo]({{ page.zenodo_link }}): > > ``` > https://zenodo.org/records/14770765/files/genome.fasta @@ -120,7 +122,7 @@ Here's how to run STAR with this specific parameter (**"Read alignement tags to > - {% icon param-file %} *"RNA-Seq FASTQ/FASTA file, forward reads"*: `rnaseq_R1.fq.gz` (Input dataset) > - {% icon param-file %} *"RNA-Seq FASTQ/FASTA file, reverse reads"*: `rnaseq_R2.fq.gz` (Input dataset) > - *"Custom or built-in reference genome"*: `Use reference genome from history and create temporary index` -> - {% icon param-file %} *"Select a reference genome"*: `genome_masked.fasta` (Input dataset) +> - {% icon param-file %} *"Select a reference genome"*: `genome.fasta` (Input dataset) > - *"Length of the SA pre-indexing string"*: `11` > - In *"BAM output format specification"*: > - In *"Read alignement tags to include in the BAM output"*: @@ -132,9 +134,9 @@ Here's how to run STAR with this specific parameter (**"Read alignement tags to We now have the following required inputs: -- A masked genome in FASTA format -- RNAseq sequence alignments in BAM format -- Protein annotation in FASTA format +- A masked genome in FASTA format: `genome.fasta` +- RNAseq sequence alignments in BAM format: `RNASeq.bam` +- Protein annotation in FASTA format: `protein_sequences.fasta` With these files, We can run [**Braker3**](https://github.com/Gaius-Augustus/BRAKER) to perform the structural annotation of the genome. @@ -142,10 +144,10 @@ With these files, We can run [**Braker3**](https://github.com/Gaius-Augustus/BRA > Genome annotation with Braker3 > > 1. {% tool [Braker3](toolshed.g2.bx.psu.edu/repos/iuc/braker3/braker3/3.0.8+galaxy0) %} with the following parameters: -> - {% icon param-file %} *"Assembly to annotate"*: `genome_masked.fasta` (Input dataset) +> - {% icon param-file %} *"Assembly to annotate"*: `genome.fasta` (Input dataset) > - *"Species name"*: `Mucor mucedo` -> - {% icon param-file %} *"RNA-seq mapped to genome to train Augustus/GeneMark"*: `rnaseq.bam` (Input dataset) -> - {% icon param-file %} *"Proteins to map to genome"*: `SwissProt_subset.fasta` (Input dataset) +> - {% icon param-file %} *"RNA-seq mapped to genome to train Augustus/GeneMark"*: `RNASeq.bam` (Input dataset) +> - {% icon param-file %} *"Proteins to map to genome"*: `protein_sequences.fasta` (Input dataset) > - {% icon param-file %} *"Fungal genome"*: select `Yes` > - *"Output format"*: `GFF3` > @@ -182,7 +184,7 @@ So first generate these sequences: > 1. {% tool [GFFread](toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.4+galaxy0) %} with the following parameters: > - {% icon param-file %} *"Input GFF3 or GTF feature file"*: output of {% tool [Braker](toolshed.g2.bx.psu.edu/repos/iuc/braker3/braker3/3.0.8+galaxy0) %} > - In *"Reference Genome"* select: `From your history` (Input dataset) -> - *"Genome Reference Fasta"*: `masked genome` (Input dataset) +> - *"Genome Reference Fasta"*: `genome.fasta` (Input dataset) > - In *"Select fasta outputs"* select: `fasta file with spliced exons for each GFF transcript (-y)` > - *"full GFF attribute preservation (all attributes are shown)"*: `Yes` > - *"decode url encoded characters within attributes"*: `Yes` @@ -218,7 +220,7 @@ The parameters for running BUSCO on the masked genome: > BUSCO in genome mode > > 1. {% tool [Busco](toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0) %} with the following parameters: -> - {% icon param-file %} *"Sequences to analyse"*: `masked genome` (Input dataset) +> - {% icon param-file %} *"Sequences to analyse"*: `genome.fasta` (Input dataset) > - *"Mode"*: `Genome assemblies (DNA)` > - *"Auto-detect or select lineage?"*: `Select lineage` > - *"Lineage"*: `Mucorales` @@ -280,7 +282,7 @@ This browser enables you to navigate along the chromosomes of the genome and vie > > 1. {% tool [JBrowse](toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1) %} with the following parameters: > - *"Reference genome to display"*: `Use a genome from history` -> - {% icon param-file %} *"Select the reference genome"*: `genome_masked.fasta` (Input dataset) +> - {% icon param-file %} *"Select the reference genome"*: `genome.fasta` (Input dataset) > - In *"Track Group"*: > - {% icon param-repeat %} *"Insert Track Group"* > - *"Track Category"*: `Annotation` From 02979991c07c51bf5642019576b95955e6ce0eaa Mon Sep 17 00:00:00 2001 From: Tristan Reynolds <31689286+tflowers15@users.noreply.github.com> Date: Mon, 6 Jul 2026 10:35:44 +1000 Subject: [PATCH 2/3] Correct GFFread to output protein fasta pep.fa --- topics/genome-annotation/tutorials/braker3/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/genome-annotation/tutorials/braker3/tutorial.md b/topics/genome-annotation/tutorials/braker3/tutorial.md index d056a14c0322b3..431cd8c9d95755 100644 --- a/topics/genome-annotation/tutorials/braker3/tutorial.md +++ b/topics/genome-annotation/tutorials/braker3/tutorial.md @@ -185,7 +185,7 @@ So first generate these sequences: > - {% icon param-file %} *"Input GFF3 or GTF feature file"*: output of {% tool [Braker](toolshed.g2.bx.psu.edu/repos/iuc/braker3/braker3/3.0.8+galaxy0) %} > - In *"Reference Genome"* select: `From your history` (Input dataset) > - *"Genome Reference Fasta"*: `genome.fasta` (Input dataset) -> - In *"Select fasta outputs"* select: `fasta file with spliced exons for each GFF transcript (-y)` +> - In *"Select fasta outputs"* select: `protein fasta file with the translation of CDS for each record (-y)` > - *"full GFF attribute preservation (all attributes are shown)"*: `Yes` > - *"decode url encoded characters within attributes"*: `Yes` > - *"warn about duplicate transcript IDs and other potential problems with the given GFF/GTF records"*: `Yes` From d1dc27fa2f0c9c4b15a27e8beec92b2d963d287a Mon Sep 17 00:00:00 2001 From: Tristan Reynolds <31689286+tflowers15@users.noreply.github.com> Date: Mon, 6 Jul 2026 11:23:48 +1000 Subject: [PATCH 3/3] Remove data library import snippet --- topics/genome-annotation/tutorials/braker3/tutorial.md | 1 - 1 file changed, 1 deletion(-) diff --git a/topics/genome-annotation/tutorials/braker3/tutorial.md b/topics/genome-annotation/tutorials/braker3/tutorial.md index 431cd8c9d95755..ea6e0ca175da77 100644 --- a/topics/genome-annotation/tutorials/braker3/tutorial.md +++ b/topics/genome-annotation/tutorials/braker3/tutorial.md @@ -99,7 +99,6 @@ To annotate our genome using Braker3, we will use the following files: > > {% snippet faqs/galaxy/datasets_import_via_link.md %} > -> {% snippet faqs/galaxy/datasets_import_from_data_library.md %} > {: .hands_on}