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Exploring results: web report & JBrowse2

To graphically explore results, splicekit provides an integrated JBrowse2 instance alongside its HTML report, both served from the same local web server.

Preparing and starting

splicekit jbrowse2 process   # process JBrowse2 files (genome, BAM tracks, etc.)
splicekit jbrowse2 start     # start the local web server

# equivalent to running both steps above:
splicekit jbrowse2

# also starts the same web server, alongside the HTML report:
splicekit web

splicekit process (the full pipeline) also runs the jbrowse2 steps automatically.

splicekit jbrowse2 process downloads and unpacks a local JBrowse2 web build the first time it runs, indexes the reference genome FASTA, and generates per-sample BigWig/CRAM tracks plus junction BED tracks from the project's BAM files.

splicekit web / splicekit jbrowse2 start then serve everything from a single local HTTP server:

  • http://<host>:8007/report — the HTML report generated by splicekit report.
  • http://<host>:8007/jbrowse2/?config=splicekit_data/config.json — the JBrowse2 genome browser, pre-configured with the project's genome and BAM/BigWig tracks.

The edgeR results tables link directly into this JBrowse2 instance via their jbrowse_url column, so you can jump straight from a significant junction/exon/gene to its genomic context.