GBrowse2(1)

💖 GBrowse2(1) 💖

okay bestie, welcome to the GBrowse2 manual page, section 1 — USER COMMANDS, and yes we're doing this whole thing together, no skimming, no skipping, we're gonna understand it 💅

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🌸 NAME 🌸

browse_import_ucsc_db — bestie, this thing Creates a framework data source ✨

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🦋 DESCRIPTION 🦋

So what it does is: it creates a framework data source for one of the genomes that the UCSC Genome Browser already knows about. Genius, iconic, no notes. After that you can go in and modify the data source configuration file, add your own data, and so forth — it's your sandbox now 🎀

You hand it the name of a UCSC genome build, and optionally a description to display in GBrowse.

To get started, find the data source you want by going to:

http://genome.ucsc.edu/cgi-bin/hgGateway

…and using the "clade" and "genome" menus to navigate to the species and build number you're obsessed with. The data source name is chilling in the blue box below the navigation controls. Look for something like this:

D. melanogaster Genome Browser – dm3 assembly (sequences)

The data source name appears right before the word "assembly" — in this case, that's "dm3" 👑

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🌈 USAGE 🌈

[options] <UCSC genome build> [<Description>]

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✨ OPTIONS ✨

To get a list of all sources recognized by UCSC appears, type:

browse_import_ucsc_db --list

Options, bestie, here they are:

• --remove-chr — Remove the 'chr' prefix from all chromosome names
• --list — List data sources

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🍓 EXAMPLE 🍓

Example:

$0 hg19 'Human genome (hg19)'

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👑 AUTHOR 👑

• Olivier Sallou (olivier.sallou (at) irisa.fr) — Man page and packaging
• Lincoln Stein — GBrowse

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and that's the whole page, you ate that fr fr 🫶 this was version 1.1.0, dated February 07, 2011 — go forth and import your genomes, main character 💜