3 posts
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: normalize and index the VCF, annotate with rsIDs and consequences, verify the genotype in the raw reads, and query millions of variants in under a second.