From 869ad65eb4b1ef38f8f353ac4504991c8494f2dd Mon Sep 17 00:00:00 2001 From: EngyNasr Date: Tue, 28 Nov 2023 14:57:59 +0100 Subject: [PATCH 01/12] adding tag microgalaxy to the microgalaxy related training --- topics/assembly/tutorials/ecoli_comparison/tutorial.md | 1 + topics/assembly/tutorials/unicycler-assembly/tutorial.md | 1 + topics/evolution/tutorials/mtb_phylogeny/tutorial.md | 1 + topics/evolution/tutorials/mtb_transmission/tutorial.md | 1 + .../tutorials/annotation-with-prokka/tutorial.md | 1 + topics/genome-annotation/tutorials/apollo/tutorial.md | 1 + topics/genome-annotation/tutorials/gene-centric/tutorial.md | 1 + .../metagenomics/tutorials/metatranscriptomics-short/tutorial.md | 1 + topics/metagenomics/tutorials/metatranscriptomics/tutorial.md | 1 + .../pathogen-detection-from-nanopore-foodborne-data/tutorial.md | 1 + topics/variant-analysis/tutorials/microbial-variants/tutorial.md | 1 + topics/variant-analysis/tutorials/non-dip/tutorial.md | 1 + .../variant-analysis/tutorials/tb-variant-analysis/tutorial.md | 1 + 13 files changed, 13 insertions(+) diff --git a/topics/assembly/tutorials/ecoli_comparison/tutorial.md b/topics/assembly/tutorials/ecoli_comparison/tutorial.md index a86d403aa4d7a4..598e39203f4194 100644 --- a/topics/assembly/tutorials/ecoli_comparison/tutorial.md +++ b/topics/assembly/tutorials/ecoli_comparison/tutorial.md @@ -11,6 +11,7 @@ requirements: - unicycler-assembly tags: - prokaryote + - microgalaxy questions: - "I just assembled a genome. How does it compare with already sequenced genomes?" - "How do I find rearranged, inserted, or deleted regions?" diff --git a/topics/assembly/tutorials/unicycler-assembly/tutorial.md b/topics/assembly/tutorials/unicycler-assembly/tutorial.md index ecd594fa856f4e..7f4196492fab57 100644 --- a/topics/assembly/tutorials/unicycler-assembly/tutorial.md +++ b/topics/assembly/tutorials/unicycler-assembly/tutorial.md @@ -6,6 +6,7 @@ zenodo_link: "https://doi.org/10.5281/zenodo.940733" level: Introductory tags: - prokaryote + - microgalaxy questions: - "I have short reads and long reads. How do I assemble a genome?" objectives: diff --git a/topics/evolution/tutorials/mtb_phylogeny/tutorial.md b/topics/evolution/tutorials/mtb_phylogeny/tutorial.md index 366c594281059b..157bca179765df 100644 --- a/topics/evolution/tutorials/mtb_phylogeny/tutorial.md +++ b/topics/evolution/tutorials/mtb_phylogeny/tutorial.md @@ -32,6 +32,7 @@ tags: - prokaryote - one-health - phylogenetics +- microgalaxy --- diff --git a/topics/evolution/tutorials/mtb_transmission/tutorial.md b/topics/evolution/tutorials/mtb_transmission/tutorial.md index 686271701d2681..9778b0db950f6c 100644 --- a/topics/evolution/tutorials/mtb_transmission/tutorial.md +++ b/topics/evolution/tutorials/mtb_transmission/tutorial.md @@ -36,6 +36,7 @@ contributions: tags: - prokaryote - one-health +- microgalaxy --- diff --git a/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.md b/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.md index d1a60720ec3865..32014ab796211e 100644 --- a/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.md +++ b/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.md @@ -5,6 +5,7 @@ title: "Genome annotation with Prokka" zenodo_link: "https://doi.org/10.5281/zenodo.1156405" tags: - prokaryote + - microgalaxy questions: - "How can we annotate a bacterial genome?" - "How can we visualize annotated genomic features?" diff --git a/topics/genome-annotation/tutorials/apollo/tutorial.md b/topics/genome-annotation/tutorials/apollo/tutorial.md index 24579d73eebec4..6f1050f9bb12cf 100644 --- a/topics/genome-annotation/tutorials/apollo/tutorial.md +++ b/topics/genome-annotation/tutorials/apollo/tutorial.md @@ -5,6 +5,7 @@ title: Refining Genome Annotations with Apollo (prokaryotes) zenodo_link: https://zenodo.org/record/4889110 tags: - prokaryote + - microgalaxy questions: - How to visualize your genome after automated annotations have been performed? - How to manually annotate genome after automated annotations have been performed? diff --git a/topics/genome-annotation/tutorials/gene-centric/tutorial.md b/topics/genome-annotation/tutorials/gene-centric/tutorial.md index be23e180466e97..45197982dd320b 100644 --- a/topics/genome-annotation/tutorials/gene-centric/tutorial.md +++ b/topics/genome-annotation/tutorials/gene-centric/tutorial.md @@ -20,6 +20,7 @@ tags: - cookbook - eukaryote - prokaryote +- microgalaxy requirements: - type: "internal" diff --git a/topics/metagenomics/tutorials/metatranscriptomics-short/tutorial.md b/topics/metagenomics/tutorials/metatranscriptomics-short/tutorial.md index 77a40c641cd545..f03bebfa1bfed0 100644 --- a/topics/metagenomics/tutorials/metatranscriptomics-short/tutorial.md +++ b/topics/metagenomics/tutorials/metatranscriptomics-short/tutorial.md @@ -30,6 +30,7 @@ contributors: - pravs3683 - shiltemann - paulzierep +- EngyNasr --- diff --git a/topics/metagenomics/tutorials/metatranscriptomics/tutorial.md b/topics/metagenomics/tutorials/metatranscriptomics/tutorial.md index 4fa3da15f4aff3..84e7b61864e8a5 100644 --- a/topics/metagenomics/tutorials/metatranscriptomics/tutorial.md +++ b/topics/metagenomics/tutorials/metatranscriptomics/tutorial.md @@ -32,6 +32,7 @@ contributors: - pravs3683 - shiltemann - paulzierep +- EngyNasr --- {% include topics/metagenomics/tutorials/metatranscriptomics/content.md short=false %} diff --git a/topics/metagenomics/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.md b/topics/metagenomics/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.md index 2c9d2ca4e9e18f..68da7c045f8191 100644 --- a/topics/metagenomics/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.md +++ b/topics/metagenomics/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.md @@ -3,6 +3,7 @@ layout: tutorial_hands_on title: "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition" tags: + - microgalaxy - Nanopore data analysis - Pathogens detection - Phylogenetic tree diff --git a/topics/variant-analysis/tutorials/microbial-variants/tutorial.md b/topics/variant-analysis/tutorials/microbial-variants/tutorial.md index caaef9e3f444e0..d1f3469123ff4d 100644 --- a/topics/variant-analysis/tutorials/microbial-variants/tutorial.md +++ b/topics/variant-analysis/tutorials/microbial-variants/tutorial.md @@ -6,6 +6,7 @@ subtopic: introduction zenodo_link: "https://doi.org/10.5281/zenodo.582600" tags: - prokaryote + - microgalaxy questions: - "How do we detect differences between a set of reads from a microorganism and a reference genome" objectives: diff --git a/topics/variant-analysis/tutorials/non-dip/tutorial.md b/topics/variant-analysis/tutorials/non-dip/tutorial.md index a82fdad7a1b6ed..49a3a07f29ff53 100644 --- a/topics/variant-analysis/tutorials/non-dip/tutorial.md +++ b/topics/variant-analysis/tutorials/non-dip/tutorial.md @@ -6,6 +6,7 @@ subtopic: introduction zenodo_link: "https://doi.org/10.5281/zenodo.1251112" tags: - prokaryote + - microgalaxy questions: - "How does frequency of mitochondrial polymorphisms change from mother to child?" objectives: diff --git a/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.md b/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.md index ef42b4b231f7b5..2889ac58320c06 100644 --- a/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.md +++ b/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.md @@ -23,6 +23,7 @@ contributors: tags: - prokaryote - one-health + - microgalaxy --- From d402f06a906f3ce004c2cf8a7b5ceb3b2fc923a1 Mon Sep 17 00:00:00 2001 From: EngyNasr Date: Tue, 28 Nov 2023 15:07:31 +0100 Subject: [PATCH 02/12] removing affliation update --- .../pathogen-detection-from-nanopore-foodborne-data/tutorial.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/topics/metagenomics/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.md b/topics/metagenomics/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.md index 68da7c045f8191..d170d2edc4a8cf 100644 --- a/topics/metagenomics/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.md +++ b/topics/metagenomics/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.md @@ -34,8 +34,6 @@ contributions: funding: - gallantries - eosc-life - affiliations: - - uni-freiburg --- From 776c608d7bae6f6a139c3a8d0c879e1e5d5c9a41 Mon Sep 17 00:00:00 2001 From: EngyNasr Date: Tue, 28 Nov 2023 15:12:52 +0100 Subject: [PATCH 03/12] removing this change as its done in another PR --- CONTRIBUTORS.yaml | 2 -- 1 file changed, 2 deletions(-) diff --git a/CONTRIBUTORS.yaml b/CONTRIBUTORS.yaml index d92e3ca781cb64..afdb2d0f6d0e3e 100644 --- a/CONTRIBUTORS.yaml +++ b/CONTRIBUTORS.yaml @@ -501,8 +501,6 @@ EngyNasr: matrix: 'EngyNasr:matrix.org' joined: 2021-05 elixir_node: de - affiliations: - - uni-freiburg ecoissac: github: false From 9142b66d696fcaeec8975fa083a7fd9dea028953 Mon Sep 17 00:00:00 2001 From: EngyNasr Date: Tue, 28 Nov 2023 15:23:29 +0100 Subject: [PATCH 04/12] adding the rest of the microgalaxy tag --- topics/metagenomics/tutorials/beer-data-analysis/tutorial.md | 1 + topics/metagenomics/tutorials/general-tutorial/tutorial.md | 2 ++ topics/metagenomics/tutorials/metagenomics-assembly/tutorial.md | 1 + .../tutorials/metatranscriptomics-short/tutorial.md | 1 + topics/metagenomics/tutorials/metatranscriptomics/tutorial.md | 1 + .../metagenomics/tutorials/mothur-miseq-sop-short/tutorial.md | 2 ++ topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.md | 2 ++ topics/proteomics/tutorials/metaproteomics/tutorial.md | 2 +- .../proteomics/tutorials/metaquantome-data-creation/tutorial.md | 2 +- topics/proteomics/tutorials/metaquantome-function/tutorial.md | 2 +- topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.md | 2 +- 11 files changed, 14 insertions(+), 4 deletions(-) diff --git a/topics/metagenomics/tutorials/beer-data-analysis/tutorial.md b/topics/metagenomics/tutorials/beer-data-analysis/tutorial.md index 7369fdbe2d53ef..4240b820772ac2 100644 --- a/topics/metagenomics/tutorials/beer-data-analysis/tutorial.md +++ b/topics/metagenomics/tutorials/beer-data-analysis/tutorial.md @@ -23,6 +23,7 @@ tags: - beer - citizen science - metagenomics +- microgalaxy contributions: authorship: - plushz diff --git a/topics/metagenomics/tutorials/general-tutorial/tutorial.md b/topics/metagenomics/tutorials/general-tutorial/tutorial.md index 79f51b639c11e2..291d2660d24b51 100644 --- a/topics/metagenomics/tutorials/general-tutorial/tutorial.md +++ b/topics/metagenomics/tutorials/general-tutorial/tutorial.md @@ -21,6 +21,8 @@ key_points: contributors: - shiltemann - bebatut +tags: + - microgalaxy --- diff --git a/topics/metagenomics/tutorials/metagenomics-assembly/tutorial.md b/topics/metagenomics/tutorials/metagenomics-assembly/tutorial.md index fb5b23863fd138..5e9cb5a4d09b05 100644 --- a/topics/metagenomics/tutorials/metagenomics-assembly/tutorial.md +++ b/topics/metagenomics/tutorials/metagenomics-assembly/tutorial.md @@ -35,6 +35,7 @@ contributions: tags: - assembly - metagenomics + - microgalaxy --- diff --git a/topics/metagenomics/tutorials/metatranscriptomics-short/tutorial.md b/topics/metagenomics/tutorials/metatranscriptomics-short/tutorial.md index f03bebfa1bfed0..4108af593de485 100644 --- a/topics/metagenomics/tutorials/metatranscriptomics-short/tutorial.md +++ b/topics/metagenomics/tutorials/metatranscriptomics-short/tutorial.md @@ -15,6 +15,7 @@ objectives: level: Introductory tags: - metatranscriptomics +- microgalaxy time_estimation: 3H key_points: - Metatranscriptomics data have the same QC profile that RNA-seq data diff --git a/topics/metagenomics/tutorials/metatranscriptomics/tutorial.md b/topics/metagenomics/tutorials/metatranscriptomics/tutorial.md index 84e7b61864e8a5..aec03e7d402af7 100644 --- a/topics/metagenomics/tutorials/metatranscriptomics/tutorial.md +++ b/topics/metagenomics/tutorials/metatranscriptomics/tutorial.md @@ -15,6 +15,7 @@ objectives: level: Introductory tags: - metatranscriptomics +- microgalaxy time_estimation: 5H key_points: - Metatranscriptomics data have the same QC profile that RNA-seq data diff --git a/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.md b/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.md index 33aa68a260b7fb..c49bbc12658b43 100644 --- a/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.md +++ b/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.md @@ -19,6 +19,8 @@ contributors: - shiltemann - bebatut - tnabtaf +tags: + - microgalaxy --- {% include topics/metagenomics/tutorials/mothur-miseq-sop/content.md short=true %} diff --git a/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.md b/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.md index a1f4fabcd8f441..b5ba85632d5583 100644 --- a/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.md +++ b/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.md @@ -19,6 +19,8 @@ contributors: - shiltemann - bebatut - tnabtaf +tags: + - microgalaxy --- {% include topics/metagenomics/tutorials/mothur-miseq-sop/content.md short=false %} diff --git a/topics/proteomics/tutorials/metaproteomics/tutorial.md b/topics/proteomics/tutorials/metaproteomics/tutorial.md index 0152d43be2a394..72a7b00c128ad7 100644 --- a/topics/proteomics/tutorials/metaproteomics/tutorial.md +++ b/topics/proteomics/tutorials/metaproteomics/tutorial.md @@ -22,7 +22,7 @@ contributors: - blankclemens - subinamehta subtopic: multi-omics -tags: [microbiome] +tags: [microgalaxy] --- In this metaproteomics tutorial we will identify expressed proteins from a complex bacterial community sample. diff --git a/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.md b/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.md index fb93d23a04c700..589ab0567b23e0 100644 --- a/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.md +++ b/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.md @@ -31,7 +31,7 @@ follow_up_training: - metaproteomics subtopic: multi-omics -tags: [microbiome] +tags: [microgalaxy] --- diff --git a/topics/proteomics/tutorials/metaquantome-function/tutorial.md b/topics/proteomics/tutorials/metaquantome-function/tutorial.md index bf25d028ea3237..dc413babe0d572 100644 --- a/topics/proteomics/tutorials/metaquantome-function/tutorial.md +++ b/topics/proteomics/tutorials/metaquantome-function/tutorial.md @@ -38,7 +38,7 @@ requirements: tutorials: - metaquantome-data-creation subtopic: multi-omics -tags: [microbiome] +tags: [microgalaxy] --- diff --git a/topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.md b/topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.md index 003aa00f9ab8c9..85659880da8ae5 100644 --- a/topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.md +++ b/topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.md @@ -35,7 +35,7 @@ requirements: - metaquantome-data-creation subtopic: multi-omics -tags: [microbiome] +tags: [microgalaxy] --- From bd3fd3d10a4339c2c55e0732d5cdfb476ad9fe82 Mon Sep 17 00:00:00 2001 From: EngyNasr Date: Tue, 28 Nov 2023 15:30:00 +0100 Subject: [PATCH 05/12] I reuined the afflication in the contributors.yaml so I added it again, I am sorryy :D --- CONTRIBUTORS.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CONTRIBUTORS.yaml b/CONTRIBUTORS.yaml index afdb2d0f6d0e3e..d92e3ca781cb64 100644 --- a/CONTRIBUTORS.yaml +++ b/CONTRIBUTORS.yaml @@ -501,6 +501,8 @@ EngyNasr: matrix: 'EngyNasr:matrix.org' joined: 2021-05 elixir_node: de + affiliations: + - uni-freiburg ecoissac: github: false From 0405a7380576bbc41e8931d4ae8b2de9f592611a Mon Sep 17 00:00:00 2001 From: Engy Nasr Date: Tue, 28 Nov 2023 16:04:54 +0100 Subject: [PATCH 06/12] Update tutorial.md correcting the linting error --- topics/assembly/tutorials/unicycler-assembly/tutorial.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/assembly/tutorials/unicycler-assembly/tutorial.md b/topics/assembly/tutorials/unicycler-assembly/tutorial.md index 7f4196492fab57..de3f41a0d9feba 100644 --- a/topics/assembly/tutorials/unicycler-assembly/tutorial.md +++ b/topics/assembly/tutorials/unicycler-assembly/tutorial.md @@ -172,7 +172,7 @@ In this example we will use a downsampled version of *E. coli* C-1 Illumina and If all goes well you will see datasets uploading and changing states from gray to green as shown below. The figure below also shows how datasets can be tagged. -![Datasets in History](../../images/starting_data.png "Sequencing data loaded into Galaxy history. The full progression from gray (scheduling) to green (all OK) state is shown. To make it easier to identify datasets as we progress through the analysis we use so-called Hashtags. To tag a dataset: click on dataset to expand it (as shown in panel four); click the tag icon () and a text field will appear. Add a tag (in this case F) pre-pended with hash (#). Hit enter. Do this for all three datasets and it will appear as in panel five.") +![Datasets in History](../../images/_data.png "Sequencing data loaded into Galaxy history. The full progression from gray (scheduling) to green (all OK) state is shown. To make it easier to identify datasets as we progress through the analysis we use so-called Hashtags. To tag a dataset: click on dataset to expand it (as shown in panel four); click the tag icon () and a text field will appear. Add a tag (in this case F) pre-pended with hash (#). Hit enter. Do this for all three datasets and it will appear as in panel five.") ### Assess Read Quality @@ -269,7 +269,7 @@ Let's look at the entire assembly and its annotation in the genome browser. We c Visualization requires a local installation of IGV. If you have IGV installed - just start it. If you don't - read on. -#### Starting IGV +### Starting IGV Go to IGV [download page](http://software.broadinstitute.org/software/igv/download) and select one of the options. The one I would try first would be **Java Web Start**. Simply click the **Launch** button for 10 GB distribution. From 911249c60efde491824d61cba1d2aaf288d8c70b Mon Sep 17 00:00:00 2001 From: Engy Nasr Date: Tue, 28 Nov 2023 16:06:44 +0100 Subject: [PATCH 07/12] Update tutorial.md correcting lint error --- topics/assembly/tutorials/unicycler-assembly/tutorial.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/assembly/tutorials/unicycler-assembly/tutorial.md b/topics/assembly/tutorials/unicycler-assembly/tutorial.md index de3f41a0d9feba..ad7248b9d24f3b 100644 --- a/topics/assembly/tutorials/unicycler-assembly/tutorial.md +++ b/topics/assembly/tutorials/unicycler-assembly/tutorial.md @@ -166,13 +166,13 @@ In this example we will use a downsampled version of *E. coli* C-1 Illumina and > > {% snippet faqs/galaxy/datasets_import_via_link.md %} > -> {% snippet faqs/galaxy/datasets_import_from_data_library.md %} +> {% snippet faqs/galaxy/datasets_import_from_library.md %} > {: .hands_on} If all goes well you will see datasets uploading and changing states from gray to green as shown below. The figure below also shows how datasets can be tagged. -![Datasets in History](../../images/_data.png "Sequencing data loaded into Galaxy history. The full progression from gray (scheduling) to green (all OK) state is shown. To make it easier to identify datasets as we progress through the analysis we use so-called Hashtags. To tag a dataset: click on dataset to expand it (as shown in panel four); click the tag icon () and a text field will appear. Add a tag (in this case F) pre-pended with hash (#). Hit enter. Do this for all three datasets and it will appear as in panel five.") +![Datasets in History](../../images/starting_data.png "Sequencing data loaded into Galaxy history. The full progression from gray (scheduling) to green (all OK) state is shown. To make it easier to identify datasets as we progress through the analysis we use so-called Hashtags. To tag a dataset: click on dataset to expand it (as shown in panel four); click the tag icon () and a text field will appear. Add a tag (in this case F) pre-pended with hash (#). Hit enter. Do this for all three datasets and it will appear as in panel five.") ### Assess Read Quality From c23481004a0c44390bb9ee34c50656e44ab1555e Mon Sep 17 00:00:00 2001 From: Engy Nasr Date: Tue, 28 Nov 2023 16:07:56 +0100 Subject: [PATCH 08/12] Update tutorial.md correcting lint error --- topics/assembly/tutorials/unicycler-assembly/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/assembly/tutorials/unicycler-assembly/tutorial.md b/topics/assembly/tutorials/unicycler-assembly/tutorial.md index ad7248b9d24f3b..88592b88ac291b 100644 --- a/topics/assembly/tutorials/unicycler-assembly/tutorial.md +++ b/topics/assembly/tutorials/unicycler-assembly/tutorial.md @@ -166,7 +166,7 @@ In this example we will use a downsampled version of *E. coli* C-1 Illumina and > > {% snippet faqs/galaxy/datasets_import_via_link.md %} > -> {% snippet faqs/galaxy/datasets_import_from_library.md %} +> {% snippet faqs/galaxy/datasets_import_from_data_library.md %} > {: .hands_on} From 90df9bf1d58b74415e942866039e69220db2a10d Mon Sep 17 00:00:00 2001 From: Engy Nasr Date: Tue, 28 Nov 2023 16:13:55 +0100 Subject: [PATCH 09/12] Update tutorial.md editing the the training to solve a linting issue --- .../tutorials/annotation-with-prokka/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.md b/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.md index 32014ab796211e..5180185696a3fe 100644 --- a/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.md +++ b/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.md @@ -27,7 +27,7 @@ subtopic: prokaryote In this section we will use a software tool called Prokka to annotate a draft genome sequence. Prokka is a “wrapper”; it collects together several pieces of software (from various authors), and so avoids “re-inventing the wheel”. -Prokka finds and annotates features (both protein coding regions and RNA genes, i.e. tRNA, rRNA) present on on a sequence. Note, Prokka uses a two-step process for the annotation of protein coding regions: first, protein coding regions on the genome are identified using [Prodigal](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848648/); second, the *function* of the encoded protein is predicted by similarity to proteins in one of many protein or protein domain databases. Prokka is a software tool that can be used to annotate bacterial, archaeal and viral genomes quickly, generating standard output files in GenBank, EMBL and gff formats. More information about Prokka can be found [here](https://github.com/tseemann/prokka). +Prokka finds and annotates features (both protein coding regions and RNA genes, i.e. tRNA, rRNA) present on on a sequence. Note, Prokka uses a two-step process for the annotation of protein coding regions: first, protein coding regions on the genome are identified using [Prodigal](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848648/); second, the *function* of the encoded protein is predicted by similarity to proteins in one of many protein or protein domain databases. Prokka is a software tool that can be used to annotate bacterial, archaeal and viral genomes quickly, generating standard output files in GenBank, EMBL and gff formats. More information about Prokka can be found in [Pokka's github link](https://github.com/tseemann/prokka). > > From 4a7fe33c5bf13cfc3755673e90812afafc521cba Mon Sep 17 00:00:00 2001 From: Engy Nasr Date: Tue, 28 Nov 2023 16:14:59 +0100 Subject: [PATCH 10/12] Update tutorial.md editing training to correct for a linting problem --- topics/genome-annotation/tutorials/gene-centric/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/genome-annotation/tutorials/gene-centric/tutorial.md b/topics/genome-annotation/tutorials/gene-centric/tutorial.md index 45197982dd320b..65c28b066fe24f 100644 --- a/topics/genome-annotation/tutorials/gene-centric/tutorial.md +++ b/topics/genome-annotation/tutorials/gene-centric/tutorial.md @@ -352,7 +352,7 @@ This is a URL pointing to one of the workflow outputs: `Mapping report` with the Running the notebook will generate two graphs explained in the next section. -### Interpreting the graphs +## Interpreting the graphs Analysis of sample data associated with this tutorial will produce the genome graph shown below. In this graph the Y-axis represents ORFs on positive (1, 2, 3 in red color) and negative (-1, -2, -3 in blue color) strands. The X-axis is genomic coordinates. Boxes represent matches between amino acid sequences of exons and ORFs they are superimposed to. The color of boxes reflect the extent of amino acid identity. The color key is shown in the left upper corner of the plot. The image is interactive so you can zoom in and out. From 65b7e944620c1c76dd92678bbd4b91ecbd4cd6b6 Mon Sep 17 00:00:00 2001 From: Engy Nasr Date: Tue, 28 Nov 2023 16:22:20 +0100 Subject: [PATCH 11/12] Update tutorial.md editing the training to fix the linting error --- .../metaquantome-function/tutorial.md | 22 +++++++++---------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/topics/proteomics/tutorials/metaquantome-function/tutorial.md b/topics/proteomics/tutorials/metaquantome-function/tutorial.md index dc413babe0d572..1f59d1156f782f 100644 --- a/topics/proteomics/tutorials/metaquantome-function/tutorial.md +++ b/topics/proteomics/tutorials/metaquantome-function/tutorial.md @@ -60,12 +60,12 @@ In this tutorial, we will learn specifically about the metaQuantome Function wor {: .agenda} -# **Pretreatments** +# Pretreatments The first step in this tutorial is to get the data from the Zenodo link provided and make sure that it is in the correct format. -## *Get data* +## Get data > Data upload > @@ -93,7 +93,7 @@ The first step in this tutorial is to get the data from the Zenodo link provided > {: .hands_on} -# **Download metaQuantome Databases** +# Download metaQuantome Databases > Run metaQuantome databases > @@ -134,7 +134,7 @@ The first step in this tutorial is to get the data from the Zenodo link provided > {: .question} -# **Create metaQuantome sample file** +# Create metaQuantome sample file The create samples file module is used to generate the samples file input file for the metaQuantome workflow. This input file is used to specify the column names used for each experimental group. These column names are referenced when handling the input data and performing statistical analysis. @@ -157,10 +157,10 @@ The create samples file module is used to generate the samples file input file f {: .hands_on} -# **Run metaQuantome** +# Run metaQuantome -## *metaQuantome: expand* +## metaQuantome: expand The expand module is the first analysis step in the metaQuantome analysis workflow, and can be run to analyze differently expressed functions in the samples. In function mode, the following information is required apart from metaQuantome databases and samples file: @@ -198,7 +198,7 @@ In function mode, the following information is required apart from metaQuantome {: .hands_on} -## *metaQuantome: filter* +## metaQuantome: filter The filter module is the second step in the metaQuantome workflow. The filter module filters the expanded terms to those that are representative of the data according to the sample parameters the user has specified. @@ -239,7 +239,7 @@ The filter module is the second step in the metaQuantome workflow. The filter mo > {: .question} -## *metaQuantome: stat* +## metaQuantome: stat > Statistical analysis of the filtered data on multiple conditions. > @@ -262,13 +262,13 @@ The filter module is the second step in the metaQuantome workflow. The filter mo > {: .hands_on} -# **Visualize your Data** +# Visualize your Data The outputs of the visualization module of metaQuantome are high-quality, publication-ready visualizations: barplots for the analysis of a single sample or experimental condition and differential abundance analysis, volcano plots, heatmaps, and principal components analysis for comparisons between two or more experimental conditions. Here were are showing 2 visualizations: **Barplot and Volcano Plot**. The Heatmap and PCA plot for multiple conditions are under development. There are two outputs of the visualization tool : an **HTML file (figure) and a tabular output containing the plot data**. -## *metaQuantome: visualize* Bar Chart +## metaQuantome: visualize Bar Chart > Bar chart visualization of Functions in T2 sample. > @@ -337,7 +337,7 @@ There are two outputs of the visualization tool : an **HTML file (figure) and a {: .hands_on} ![T7_MF](../../images/T7-mf.png "Top five differentially expressed Molecular Function GO terms for sample T7."){: width="85%"} -## *metaQuantome: visualize* Volcano Plots +## metaQuantome: visualize Volcano Plots > Volcano Plot visualization of the data T7 and T2. > From 9b8b6ede60a5a540c1db0ced6502945d60ad12c4 Mon Sep 17 00:00:00 2001 From: Engy Nasr Date: Tue, 28 Nov 2023 16:27:14 +0100 Subject: [PATCH 12/12] Update tutorial.md editing training to correct its format linting errors --- .../metaquantome-taxonomy/tutorial.md | 22 +++++++++---------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.md b/topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.md index 85659880da8ae5..f5cbee103a5e89 100644 --- a/topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.md +++ b/topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.md @@ -58,12 +58,12 @@ To demonstrate the use of this workflow, we have used a thermophilic biogas reac {: .agenda} -# **Pretreatments** +# Pretreatments The first step in this tutorial is to get the data from the Zenodo link provided and make sure that it is in the correct format. -## *Get data* +## Get data > Data upload > @@ -91,7 +91,7 @@ The first step in this tutorial is to get the data from the Zenodo link provided > {: .hands_on} -# **Download metaQuantome Databases** +# Download metaQuantome Databases > Run metaQuantome databases > @@ -132,7 +132,7 @@ The first step in this tutorial is to get the data from the Zenodo link provided > {: .question} -# **Create metaQuantome sample file** +# Create metaQuantome sample file The create samples file module is used to generate the samples file input file for the metaQuantome workflow. This input file is used to specify the column names used for each experimental group. These column names are referenced when handling the input data and performing statistical analysis. @@ -155,10 +155,10 @@ The create samples file module is used to generate the samples file input file f {: .hands_on} -# **Run metaQuantome** +# Run metaQuantome -## *metaQuantome: expand* +## metaQuantome: expand The expand module is the first analysis step in the metaQuantome analysis workflow, and can be run to analyze differently expressed Taxa in the samples. In taxonomy mode, the following information is required apart from metaQuantome databases and samples file: a tab-separated taxonomy annotation file, with a peptide column and a taxonomy annotation column. The taxonomic annotations should be the lowest common ancestor (LCA) for each peptide, preferably given as NCBI taxonomy IDs. @@ -197,7 +197,7 @@ In taxonomy mode, the following information is required apart from metaQuantome {: .hands_on} -## *metaQuantome: filter* +## metaQuantome: filter The filter module is the second step in the metaQuantome workflow. The filter module filters the expanded terms to those that are representative of the data according to the sample parameters the user has specified. @@ -235,7 +235,7 @@ The filter module is the second step in the metaQuantome workflow. The filter mo > {: .question} -## *metaQuantome: stat* +## metaQuantome: stat > Statistical analysis of the filtered data on multiple conditions. > @@ -259,13 +259,13 @@ The filter module is the second step in the metaQuantome workflow. The filter mo {: .hands_on} -# **Visualize your Data** +# Visualize your Data The outputs of the visualization module of metaQuantome are high-quality, publication-ready visualizations: barplots for the analysis of a single sample or experimental condition and differential abundance analysis, volcano plots, heatmaps, and principal components analysis for comparisons between two or more experimental conditions. Here were are showing 2 visualizations: **Barplot and Volcano Plot**. The Heatmap and PCA plot for multiple conditions are under development. There are two outputs of the visualization tool : an **HTML file (figure) and a tabular output containing the plot data**. -## *metaQuantome: visualize* +## metaQuantome: visualize > Bar chart visualization of Taxonomy in T2 sample. > @@ -336,7 +336,7 @@ There are two outputs of the visualization tool : an **HTML file (figure) and a ![T4_taxa](../../images/T4_taxa.png "Bar Chart visualization of Top 5 genus present in T4 sample."){: width="85%"} -## *metaQuantome: visualize* Volcano Plots +## metaQuantome: visualize Volcano Plots > Volcano Plot visualization of the data T4 and T2. >