Learner Profiles
Priya PostDoc
Priya is a postdoctoral researcher in a wet-lab group that recently started generating its own sequencing data. She is comfortable interpreting summary statistics and plots from a bioinformatics core, but has never looked at raw aligned reads or variant calls herself. A recent RNA-seq experiment produced a result she doesn’t fully trust, and she wants to be able to check it herself rather than only relying on a collaborator’s pipeline output.
This course will teach Priya how to load her own BAM and VCF files into IGV and interpret what she sees well enough to sanity-check a pipeline result. She is most interested in the alignment/SNP and RNA-seq episodes. After the workshop, Priya will be able to load her lab’s sequencing data into IGV, navigate to a specific gene or variant of interest, and judge for herself whether a candidate variant or splicing event looks convincing or looks like an artifact.
Sam Sysadmin-Turned-Analyst
Sam has a background in IT and recently moved into a bioinformatics support role. He is very comfortable with computers and file formats in the abstract, but has limited biology background and has never used a genome browser. He needs to be able to help researchers troubleshoot “why doesn’t my file load in IGV” and similar questions.
This course will give Sam a working mental model of how IGV organizes data (genomes, tracks, file formats) so that he can reason about and debug loading problems. He is particularly interested in the file-format overview and the “load your own genome” episode. After the workshop, Sam will be able to identify which IGV menu to use for a given file type, explain why a genome loaded from a bare FASTA file has no gene names, and guide a researcher through loading their own data.
Alex Analyst
Alex is a master’s student doing a genomics-focused research project. They have taken an introductory bioinformatics course and are comfortable with the command line, but their course covered alignment and variant calling only as command-line tools, without much emphasis on visual inspection. Their supervisor has asked them to visually confirm a handful of candidate variants before including them in a manuscript.
This course will give Alex the specific IGV skills needed to inspect candidate SNPs and structural signals by eye. They are most interested in the alignment/SNP episode and the wrap-up’s pointer to structural variants. After the workshop, Alex will be able to load a BAM file alongside a list of candidate variants, use sorting and coloring options to judge whether each variant looks genuine, and communicate that judgment (with a screenshot) to their supervisor.