From fe1320a095e49be94cb60d1cdeac5ef67567def5 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Thu, 3 Mar 2022 12:58:29 +0100 Subject: [PATCH 1/2] add FAQs for proteogenomics tutorial --- .../faqs/alignment_tools.md | 9 +++++++++ .../faqs/chromosome_names.md | 9 +++++++++ .../faqs/proteogenomics_example_histories.md | 20 +++++++++++++++++++ .../faqs/proteogenomics_own_data.md | 10 ++++++++++ .../faqs/proteogenomics_querytabular.md | 17 ++++++++++++++++ .../faqs/proteogenomics_variants.md | 10 ++++++++++ .../faqs/variant_mapping_file.md | 9 +++++++++ .../proteogenomics-dbsearch/faqs/mvp.md | 11 ++++++++++ .../faqs/proteogenomics_example_histories.md | 1 + .../faqs/proteogenomics_own_data.md | 1 + .../faqs/proteogenomics_querytabular.md | 1 + .../faqs/proteogenomics_variants.md | 1 + .../faqs/search_gui.md | 11 ++++++++++ .../faqs/proteogenomics_example_histories.md | 1 + .../faqs/proteogenomics_own_data.md | 1 + .../faqs/proteogenomics_querytabular.md | 1 + .../faqs/proteogenomics_variants.md | 1 + 17 files changed, 114 insertions(+) create mode 100644 topics/proteomics/tutorials/proteogenomics-dbcreation/faqs/alignment_tools.md create mode 100644 topics/proteomics/tutorials/proteogenomics-dbcreation/faqs/chromosome_names.md create mode 100644 topics/proteomics/tutorials/proteogenomics-dbcreation/faqs/proteogenomics_example_histories.md create mode 100644 topics/proteomics/tutorials/proteogenomics-dbcreation/faqs/proteogenomics_own_data.md create mode 100644 topics/proteomics/tutorials/proteogenomics-dbcreation/faqs/proteogenomics_querytabular.md create mode 100644 topics/proteomics/tutorials/proteogenomics-dbcreation/faqs/proteogenomics_variants.md create mode 100644 topics/proteomics/tutorials/proteogenomics-dbcreation/faqs/variant_mapping_file.md create mode 100644 topics/proteomics/tutorials/proteogenomics-dbsearch/faqs/mvp.md create mode 120000 topics/proteomics/tutorials/proteogenomics-dbsearch/faqs/proteogenomics_example_histories.md create mode 120000 topics/proteomics/tutorials/proteogenomics-dbsearch/faqs/proteogenomics_own_data.md create mode 120000 topics/proteomics/tutorials/proteogenomics-dbsearch/faqs/proteogenomics_querytabular.md create mode 120000 topics/proteomics/tutorials/proteogenomics-dbsearch/faqs/proteogenomics_variants.md create mode 100644 topics/proteomics/tutorials/proteogenomics-dbsearch/faqs/search_gui.md create mode 120000 topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/faqs/proteogenomics_example_histories.md create mode 120000 topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/faqs/proteogenomics_own_data.md create mode 120000 topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/faqs/proteogenomics_querytabular.md create mode 120000 topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/faqs/proteogenomics_variants.md diff --git a/topics/proteomics/tutorials/proteogenomics-dbcreation/faqs/alignment_tools.md b/topics/proteomics/tutorials/proteogenomics-dbcreation/faqs/alignment_tools.md new file mode 100644 index 00000000000000..de91fefb6a67b6 --- /dev/null +++ b/topics/proteomics/tutorials/proteogenomics-dbcreation/faqs/alignment_tools.md @@ -0,0 +1,9 @@ +--- +title: Is it possible to replace the existing alignment tools such as HISAT and Freebayes with other tools? +box_type: question +layout: faq +contributors: [subinamehta] +--- + +The tools in this workflow are customizable, however, the user has to ensure that the inputs are in the correct format, while using the same reference genome database. + diff --git a/topics/proteomics/tutorials/proteogenomics-dbcreation/faqs/chromosome_names.md b/topics/proteomics/tutorials/proteogenomics-dbcreation/faqs/chromosome_names.md new file mode 100644 index 00000000000000..d6a16e322ef2e3 --- /dev/null +++ b/topics/proteomics/tutorials/proteogenomics-dbcreation/faqs/chromosome_names.md @@ -0,0 +1,9 @@ +--- +title: Why do we change the chromosome names in the Ensembl GTF to match the UCSC genome reference? +box_type: question +layout: faq +contributors: [subinamehta] +--- + +UCSC chromosome names begin with the prefix `chr`, but Ensembl chromosome names do not. For example, chromosome 19 would be denoted as `chr19` in UCSC, and as `19` in Ensemble. Most tools would view those as different when looking for matches/overlaps. Therefore it is always a good idea to make sure these match before you perform any downstream analysis. + diff --git a/topics/proteomics/tutorials/proteogenomics-dbcreation/faqs/proteogenomics_example_histories.md b/topics/proteomics/tutorials/proteogenomics-dbcreation/faqs/proteogenomics_example_histories.md new file mode 100644 index 00000000000000..39b72086ca04a0 --- /dev/null +++ b/topics/proteomics/tutorials/proteogenomics-dbcreation/faqs/proteogenomics_example_histories.md @@ -0,0 +1,20 @@ +--- +title: Example histories for the proteogenomics tutorials +area: proteogenomics general +box_type: tip +layout: faq +contributors: [subinamehta] +--- + +If you get stuck or would like to see what the results should look like, you can have a look at one of the following public histories: + +Galaxy EU (usegalaxy.eu): +- History1: [Part 1: database creation](https://usegalaxy.eu/u/galaxyp/h/proteogenomics-1-database-creation) +- History2: [Part 2: database search](https://usegalaxy.eu/u/galaxyp/h/proteogenomics-2-database-search) +- History3: [Part3: novel peptide analysis](https://usegalaxy.eu/u/galaxyp/h/proteogenomics-3-novel-peptide-analysis) + +Galaxy Main (usegalaxy.org): +- History 1: [Part 1: database creation](https://usegalaxy.org/u/nate/h/imported-from-usegalaxyeu-proteogenomics-1-database-creation) +- History 2: [Part 2: database search](https://usegalaxy.org/u/nate/h/imported-from-usegalaxyeu-proteogenomics-2-database-search) +- History 3: [Part 3: novel peptide analysis](https://usegalaxy.org/u/nate/h/imported-from-usegalaxyeu-proteogenomics-3-novel-peptide-analysis) + diff --git a/topics/proteomics/tutorials/proteogenomics-dbcreation/faqs/proteogenomics_own_data.md b/topics/proteomics/tutorials/proteogenomics-dbcreation/faqs/proteogenomics_own_data.md new file mode 100644 index 00000000000000..1c52fcd08c1467 --- /dev/null +++ b/topics/proteomics/tutorials/proteogenomics-dbcreation/faqs/proteogenomics_own_data.md @@ -0,0 +1,10 @@ +--- +title: Can I use these workflows on datasets generated from our laboratory? +area: proteogenomics general +box_type: question +layout: faq +contributors: [subinamehta] +--- + +Yes, the workflows can be used on other datasets as well. However, you will need to consider data acquisition and sample preparation methods so that the tool parameters can be adjusted accordingly. + diff --git a/topics/proteomics/tutorials/proteogenomics-dbcreation/faqs/proteogenomics_querytabular.md b/topics/proteomics/tutorials/proteogenomics-dbcreation/faqs/proteogenomics_querytabular.md new file mode 100644 index 00000000000000..adf706fe62e548 --- /dev/null +++ b/topics/proteomics/tutorials/proteogenomics-dbcreation/faqs/proteogenomics_querytabular.md @@ -0,0 +1,17 @@ +--- +title: The workflows contain several Query tabular for text manipulation, is there a tutorial for that? +area: proteogenomics general +box_type: question +layout: faq +contributors: [subinamehta] +--- + +Query tabular loads a tabular database and creates a sqlite database and tabular file. To learn more about SQL Queries - please look at [this documentation](https://www.sqlite.org/docs.html). + +The help section on the Query Tabular tool provides simple examples of both filtering the input tabular datasets, as well as examples of SQL queries. Query Tabular also incorporates regex functions that can be used queries. The PSM report datasets in these tutorials have fields that are lists of protein IDs. + +Query Tabular help shows how to normalize those protein list fields so that we can perform operations by protein ID. See section: *Normalizing by Line Filtering into 2 Tables* in the tool help (below the tool in Galaxy). + + + + diff --git a/topics/proteomics/tutorials/proteogenomics-dbcreation/faqs/proteogenomics_variants.md b/topics/proteomics/tutorials/proteogenomics-dbcreation/faqs/proteogenomics_variants.md new file mode 100644 index 00000000000000..d1819a4b1336ba --- /dev/null +++ b/topics/proteomics/tutorials/proteogenomics-dbcreation/faqs/proteogenomics_variants.md @@ -0,0 +1,10 @@ +--- +title: What kind of variants are seen in the output? +area: proteogenomics general +box_type: question +layout: faq +contributors: [subinamehta] +--- + +From this workflow we can see insertions, deletions, SNVs, or we will know whether it's an intron, exon, splice junction etc. + diff --git a/topics/proteomics/tutorials/proteogenomics-dbcreation/faqs/variant_mapping_file.md b/topics/proteomics/tutorials/proteogenomics-dbcreation/faqs/variant_mapping_file.md new file mode 100644 index 00000000000000..021f80dca430ea --- /dev/null +++ b/topics/proteomics/tutorials/proteogenomics-dbcreation/faqs/variant_mapping_file.md @@ -0,0 +1,9 @@ +--- +title: Why do we have a variant mapping file when it is not being used in the workflow? +box_type: question +layout: faq +contributors: [subinamehta] +--- + +We are working on updating the existing annotation tool to include the variant mapping file. Once that is done, the variant mapping file will also be an input for those tools. + diff --git a/topics/proteomics/tutorials/proteogenomics-dbsearch/faqs/mvp.md b/topics/proteomics/tutorials/proteogenomics-dbsearch/faqs/mvp.md new file mode 100644 index 00000000000000..94599a056f3242 --- /dev/null +++ b/topics/proteomics/tutorials/proteogenomics-dbsearch/faqs/mvp.md @@ -0,0 +1,11 @@ +--- +title: In the MVP platform, is it possible to view the genomic location of all the peptides? +box_type: question +layout: faq +contributors: [subinamehta] +--- + +Not really, you can only view the genomic localization of the peptides that were present in the genomic mapping file (output from the first workflow). + + + diff --git a/topics/proteomics/tutorials/proteogenomics-dbsearch/faqs/proteogenomics_example_histories.md b/topics/proteomics/tutorials/proteogenomics-dbsearch/faqs/proteogenomics_example_histories.md new file mode 120000 index 00000000000000..e0eba8c4b448d7 --- /dev/null +++ b/topics/proteomics/tutorials/proteogenomics-dbsearch/faqs/proteogenomics_example_histories.md @@ -0,0 +1 @@ +../../proteogenomics-dbcreation/faqs/proteogenomics_example_histories.md \ No newline at end of file diff --git a/topics/proteomics/tutorials/proteogenomics-dbsearch/faqs/proteogenomics_own_data.md b/topics/proteomics/tutorials/proteogenomics-dbsearch/faqs/proteogenomics_own_data.md new file mode 120000 index 00000000000000..c5eb2cc4da2072 --- /dev/null +++ b/topics/proteomics/tutorials/proteogenomics-dbsearch/faqs/proteogenomics_own_data.md @@ -0,0 +1 @@ +../../proteogenomics-dbcreation/faqs/proteogenomics_own_data.md \ No newline at end of file diff --git a/topics/proteomics/tutorials/proteogenomics-dbsearch/faqs/proteogenomics_querytabular.md b/topics/proteomics/tutorials/proteogenomics-dbsearch/faqs/proteogenomics_querytabular.md new file mode 120000 index 00000000000000..98985ef3fcb453 --- /dev/null +++ b/topics/proteomics/tutorials/proteogenomics-dbsearch/faqs/proteogenomics_querytabular.md @@ -0,0 +1 @@ +../../proteogenomics-dbcreation/faqs/proteogenomics_querytabular.md \ No newline at end of file diff --git a/topics/proteomics/tutorials/proteogenomics-dbsearch/faqs/proteogenomics_variants.md b/topics/proteomics/tutorials/proteogenomics-dbsearch/faqs/proteogenomics_variants.md new file mode 120000 index 00000000000000..022fe3e7c5381f --- /dev/null +++ b/topics/proteomics/tutorials/proteogenomics-dbsearch/faqs/proteogenomics_variants.md @@ -0,0 +1 @@ +../../proteogenomics-dbcreation/faqs/proteogenomics_variants.md \ No newline at end of file diff --git a/topics/proteomics/tutorials/proteogenomics-dbsearch/faqs/search_gui.md b/topics/proteomics/tutorials/proteogenomics-dbsearch/faqs/search_gui.md new file mode 100644 index 00000000000000..2de25331113fd6 --- /dev/null +++ b/topics/proteomics/tutorials/proteogenomics-dbsearch/faqs/search_gui.md @@ -0,0 +1,11 @@ +--- +title: How many search engines can you use in SearchGUI? +box_type: question +layout: faq +contributors: [subinamehta] +--- + +SearchGUI has options to use upto 9 search algorithms. However, running all at the same time can be time consuming. According to our initial test, upto 4 search engines can give you good results. + + + diff --git a/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/faqs/proteogenomics_example_histories.md b/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/faqs/proteogenomics_example_histories.md new file mode 120000 index 00000000000000..e0eba8c4b448d7 --- /dev/null +++ b/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/faqs/proteogenomics_example_histories.md @@ -0,0 +1 @@ +../../proteogenomics-dbcreation/faqs/proteogenomics_example_histories.md \ No newline at end of file diff --git a/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/faqs/proteogenomics_own_data.md b/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/faqs/proteogenomics_own_data.md new file mode 120000 index 00000000000000..c5eb2cc4da2072 --- /dev/null +++ b/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/faqs/proteogenomics_own_data.md @@ -0,0 +1 @@ +../../proteogenomics-dbcreation/faqs/proteogenomics_own_data.md \ No newline at end of file diff --git a/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/faqs/proteogenomics_querytabular.md b/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/faqs/proteogenomics_querytabular.md new file mode 120000 index 00000000000000..98985ef3fcb453 --- /dev/null +++ b/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/faqs/proteogenomics_querytabular.md @@ -0,0 +1 @@ +../../proteogenomics-dbcreation/faqs/proteogenomics_querytabular.md \ No newline at end of file diff --git a/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/faqs/proteogenomics_variants.md b/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/faqs/proteogenomics_variants.md new file mode 120000 index 00000000000000..022fe3e7c5381f --- /dev/null +++ b/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/faqs/proteogenomics_variants.md @@ -0,0 +1 @@ +../../proteogenomics-dbcreation/faqs/proteogenomics_variants.md \ No newline at end of file From e906a659e4f12ff0057897d771033e6060453de7 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Thu, 3 Mar 2022 13:02:30 +0100 Subject: [PATCH 2/2] hide default faqs on galaxy and gtn faq pages --- _layouts/faq-page.html | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/_layouts/faq-page.html b/_layouts/faq-page.html index 6c962dad564e36..37a442f1c506e7 100644 --- a/_layouts/faq-page.html +++ b/_layouts/faq-page.html @@ -45,6 +45,7 @@

{{q.title}} General Questions

@@ -55,8 +56,8 @@

Can't find one of the tools for this tutorial? Running into an error?

{% snippet /faqs/galaxy/analysis_troubleshooting.md %} {% endif %} - +{% endunless %}