Priya's Thursday, Two Ways
8 lessons · 22 prompts
A day in the life of a Bioinformatician: what changes with these prompts.
Track progress as a memberPriya, a bioinformatician at a small genomics lab.
On a normal Thursday, Priya starts with a failed RNA-seq pipeline. The aligner stopped partway through with an error about a missing index. She checks logs, pings the cluster admin, and loses the morning. The methods section waits, and the collaborator emails again.
With the course, she opens ChatGPT and pastes the exact error plus the command. She asks the Troubleshoot Pipeline Errors prompt for likely causes. It points to a path mismatch. She fixes it and reruns. Next she uses Write and Debug Code in Claude to adjust a small Python script that counts reads in a BAM file.
After lunch, a VCF file from a new sample will not load in her browser. She tries the Handle Biological File Formats prompt in Gemini. It shows her a bcftools view command to filter to chromosome 7 and write a smaller file. Then she uses Interpret QC and Results to turn a DESeq2 output table into a short summary for her collaborator.
By late afternoon, the pipeline is running, the methods section has a clear draft, and the collaborator has numbers to review. Priya uses the time won back to walk through the raw alignment plots, check two strange samples, and leave on time for her climbing class.
Before
- Logs open in too many tabs
- A failed run blocks the whole day
- Methods section waits until Friday
- Collaborator asks for updates again
After this course
- Error traced in one short chat
- Pipeline reruns before the next meeting
- QC summary sent to collaborator
- Home on time for climbing class
What you'll learn
- Decode Errors: Turn a cryptic tool error into a plain list of likely causes and next checks.
- Fix Code: Get help writing, correcting, or translating Python, R, and shell snippets for data tasks.
- Handle Formats: Parse, filter, and convert SAM, VCF, GFF, and other common biological files.
- Choose Statistics: Ask for plain explanations of tests and help matching a method to your question.
- Plan Analyses: Build a workflow skeleton and tool list from a biological question.
- Read QC Results: Summarize QC reports and differential expression results for yourself or collaborators.
- Make Figures: Pick a plot and get code for clear figures ready for review or publication.
- Write Clearly: Draft methods text, pipeline notes, and paper summaries in a useful first pass.
How this course works
- 8 lessonsOne task of your job each, from troubleshoot pipeline errors to document and communicate.
- Ready-to-paste promptsCopy, fill in the parts in {{brackets}}, paste into ChatGPT, Claude or Gemini.
- Tick and completeTick the prompts you tried and mark each lesson complete.
- Get certifiedFinish and keep the prompts as your own library.