Tag: igv

A practical guide to opening and inspecting BAM alignment files: samtools on the command line, IGV for visual review, and the checks worth running before you trust a variant call.

A practical guide to setting up the Integrative Genomics Viewer for personal whole-genome, RNA-seq, and copy-number data, including file indexing, pileup interpretation, batch scripting, and the failure modes that produce false confidence.

A practical guide to genome visualization tools for your own sequencing data, from IGV and the UCSC browser to igv.js, with the files each one needs.

A practical guide to loading your own whole-genome alignments, variant calls, and RNA coverage into a local genome browser, indexing the files correctly, and querying annotation programmatically instead of clicking through a web UI.

A working guide to loading your own BAM/CRAM, VCF, and RNA-seq files into IGV and igv.js: reference builds, indexing, annotation tracks, batch screenshots, and the visual checks that catch bad variant calls.

A practical setup for loading your own WGS alignments, variant calls, and RNA-seq coverage into IGV and igv.js, with the indexing, reference-build, and chromosome-naming details that usually break first.

A genome explorer is a coordinate browser plus a query layer over your own alignments and variant calls. Here is the stack we would use on a personal 30x whole genome, with the commands, file formats, and failure modes.

A working guide to building the handful of plots that matter for a personal molecular dataset: coverage tracks, variant pileups, copy-number profiles, expression MA and volcano plots, and a genome-wide circular summary. With real commands, file formats, and the failure modes that produce misleading pictures.

A working setup for looking up any SNP in your own sequencing data. Covers indexing the VCF, annotating with rsIDs and verifying genotypes in the reads.