links-bed

name	links-bed
description	Use when you need to generate HTML links to UCSC Genome Browser from BED, GFF, or VCF feature files.
disable-model-invocation	true
user-invocable	true

links-bed

Quick Start

• Command: linksBed -i intervals.bed [options] > links.html
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/linksBed
• Full reference: See references/help.md

When To Use This Tool

• Generate clickable UCSC Genome Browser links for an interval file.
• Create lightweight HTML for manual browsing of genomic coordinates.
• Point links at a local UCSC mirror instead of the public site.
• Override organism and assembly when the defaults are wrong for your dataset.

Common Patterns

# 1) Create UCSC links with defaults
linksBed \
  -i peaks.bed > peaks.links.html

# 2) Target a different organism / assembly
linksBed \
  -i peaks.bed \
  -org mouse \
  -db mm10 > peaks.mm10.links.html

# 3) Point links at a local UCSC mirror
linksBed \
  -i peaks.bed \
  -base http://mymirror.example.org \
  -org human \
  -db hg38 > peaks.local.links.html

Recommended Workflow

1. Confirm the interval file uses coordinates compatible with the intended UCSC assembly.
2. Override -org and -db explicitly for modern datasets instead of accepting the defaults.
3. Open the generated HTML and spot-check a few links before sharing it.
4. Treat this as a browsing convenience tool, not a primary data export format.

Guardrails

• The defaults are human and hg18, which are usually wrong for current work.
• -base only changes the browser hostname; it does not validate that your mirror has the chosen assembly.
• Output is HTML written to stdout, so redirect it to a file.
• Input should be BED / GFF / VCF-like coordinates that UCSC can interpret sensibly.
• Prefer -h for help; GNU-style --help / --version calls on these wrappers are noisy.