Jennifer Hillman-Jackson

Contributions

The following list includes only slides and tutorials where the individual or organisation has been added to the contributor list. This may not include the sum total of their contributions to the training materials (e.g. GTN css or design, tutorial datasets, workflow development, etc.) unless described by a news post.

Editorial Roles

This contributor has taken on additional responsibilities as an editor for the following topics. They are responsible for ensuring that the content is up to date, accurate, and follows GTN best practices.

• Using Galaxy and Managing your Data
• Introduction to Galaxy Analyses

Tutorials

• Introduction to Galaxy Analyses / Galaxy Basics for everyone 🧐
• Variant Analysis / Microbial Variant Calling 🧐

Slides

• Introduction to Galaxy Analyses / Introduction to Galaxy 🧐

FAQs

• How do I create an account on a public Galaxy instance?
• How can I reduce quota usage while still retaining prior work (data, tools, methods)?
• How to update account preferences?
• Extended Help for Differential Expression Analysis Tools
• Reporting usage problems, security issues, and bugs
• Incomplete Dataset Download
• How to find and correct tool errors related to Metadata?
• Finding BAM dataset identifiers
• Directly obtaining UCSC sourced *genome* identifiers
• Mismatched Chromosome identifiers and how to avoid them
• How to set Data Privacy Features?
• Downloading datasets
• Downloading datasets using command line
• Finding Datasets
• How to hide datasets?
• Different dataset icons and their usage
• Understanding job statuses
• Moving datasets between Galaxy servers
• Datasets not downloading at all
• Purging datasets
• Quotas for datasets and histories
• Working with deleted datasets
• Working with very large fasta datasets
• Working with very large fastq datasets
• Working with GFF GFT GTF2 GFF3 reference annotation
• Using compressed fastq data as tool inputs
• Best practices for loading fastq data into Galaxy
• How do `fastq.gz` datasets relate to the `.fastqsanger` datatype metadata assignment?
• How to format fastq data for tools that require .fastqsanger format?
• Identifying and formatting Tabular Datasets
• Understanding Datatypes
• How can I upload data using EBI-SRA?
• Data retrieval with “NCBI SRA Tools” (fastq-dump)
• NCBI SRA sourced fastq data
• Ways to use Galaxy
• How can I load data?
• Downloading histories
• Find all Histories and purge (aka permanently delete)
• Finding Histories
• Finding and working with "Histories shared with me"
• Transfer entire histories from one Galaxy server to another
• Unsharing unwanted histories
• How to use Custom Reference Genomes?
• Sorting Reference Genome
• Troubleshooting Custom Genome fasta
• Where is the tool help?
• Sorting Tools
• Tool doesn't recognize input datasets
• Understanding 'canceled by admin' or cluster failure error messages
• Understanding 'exceeds memory allocation' error messages
• Understanding input error messages
• Understanding ValueError error messages
• Understanding walltime error messages
• Does your account usage quota seem incorrect?
• Forgot Password
• Changing acount email or password

GitHub Activity

github Issues Reported

25 Merged Pull Requests

See all of the github Pull Requests and github Commits by Jennifer Hillman-Jackson.

• Reorder parameters to match tool form
  introduction
• Correct typo
  data-science
• Update for newer Data menu histories_transfer_entire_histories_from_o…
  faqs
• Update analysis_differential_expression_help.md new link type and minor reorg
  faqs
• Update analysis_differential_expression_help.md
  faqs

Reviewed 21 PRs

We love our community reviewing each other's work!

• Update for newer Data menu histories_transfer_entire_histories_from_o…
  faqs
• Update analysis_differential_expression_help.md new link type and minor reorg
  faqs
• Update reference_genomes_custom_genomes.md
  template-and-tools
  faqs
• Update reference_genomes_custom_genomes.md
  faqs
• Update analysis_differential_expression_help.md
  faqs

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