Colin Diesh cmdcolin

JBrowse 2 has a special "view type" called the "breakpoint split view" that allows you to see the connection between split long reads (e.g. SA tag) and paired-end reads

Ways to access the breakpoint split view

Using the SV inspector to launch a breakpoint split view

The SV inspector lets you load a VCF containing SV calls and then will launch a "breakpoint split view". Note that the breakpoint split view that it launches will be empty but you can then add your BAM or CRAM reads to it (on both top and bottom levels sometimes is needed)

Jaws 2 - 0:38:00
Jaws 2 - 0:54:00
Beverley hills cop - 0:55:00
Twister - 0:01:51
Twister - 1:09:00
Walton Christmas - 1:28:40
Don't Look Up - end of movie

program	size	time	mean	sd
biojsmsa	1024	1.7980085814	1.7634212551000001	0.054614392814706154
biojsmsa	1024	1.7561014924	1.7634212551000001	0.054614392814706154
biojsmsa	1024	1.7711577354	1.7634212551000001	0.054614392814706154
biojsmsa	1024	1.6753254374000002	1.7634212551000001	0.054614392814706154
biojsmsa	1024	1.7957582314	1.7634212551000001	0.054614392814706154
biojsmsa	1024	1.8305949124	1.7634212551000001	0.054614392814706154
biojsmsa	1024	1.8173887264	1.7634212551000001	0.054614392814706154
biojsmsa	1024	1.7924422974	1.7634212551000001	0.054614392814706154
biojsmsa	1024	1.6920777054	1.7634212551000001	0.054614392814706154

What does RNA-seq look like in the genome browser?

here is a picture of a "RNA-seq BAM file" in JBrowse 2

(live link https://jbrowse.org/code/jb2/v2.16.1/?config=test_data%2Fconfig_demo.json&session=share-i3nrunRxkg&password=S1tAc)

you can see that there are all these little grey boxes and the black lines connecting them. These are the so-called "reads" in the RNA-seq BAM file! there is also a little "histogram" along the top. This is showing how many "reads" mapped to a given position in the genome

	import eslint from '@eslint/js'
	import importPlugin from 'eslint-plugin-import'
	import eslintPluginReact from 'eslint-plugin-react'
	import eslintPluginReactHooks from 'eslint-plugin-react-hooks'
	import tseslint from 'typescript-eslint'

	export default tseslint.config(
	{
	// might be able to find a way to not ignore some of these but i just ignore them
	ignores: [

	jason lescalleet - the pilgrim https://www.youtube.com/watch?v=lU6PbEg6YRk (dedicated to his dad, over an hour of morbid ambience and then harsh noise)
	j peterson https://www.youtube.com/watch?v=eVX7DkYr_oA (weird ambient that also explores morbid themes in his other works)
	mattias gustaffson https://youtu.be/0pxzWUbuzYo (dark tape manipulations)
	morgan hall - skid row palace https://youtu.be/2gfBktiURew (muted dark ambient power electronics)
	all of korea undok group stuff https://soundcloud.com/korea-undok-group
	work/death - mulberries ripen and rot side b midway thru particularly dragging
	hazl fog https://youtu.be/zjqZWejfOmE (everything makade star and b.p.)
	prurient - sexual magic (erik satie reinterpreted by prurient. also entire prurient backcatalog)
	the humble bee - morning music https://youtu.be/leu6YmRWS2s (soft tape music for healing)
	gordan wilson - https://iatrogenesis.bandcamp.com/track/american-ulterior (and entire gordon/oscillating innards backcatalog)

	const fs = require("fs");
	const trackList = JSON.parse(fs.readFileSync("./trackList.json", "utf8"));

	const newTracks = [];
	const unconverted = [];

	function basicData(track) {
	return {
	name: track.key \|\| track.label,
	trackId: track.label,

	$ git clone https://github.com/goodarzilab/lorna-sh
	$ cd lorna-sh

	## look around...i decided to try starting in processing_seqs
	$ find .
	$ cd processing_seqs

	## in R repl, install dependencies
	## data.table
	## optparse