# Bioconductor Rtracklayer

> Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/imp

- Skill: `biomate-ai/bioconductor-rtracklayer` (Agent Skill)
- Install (CLI): `npx skillmds@latest add biomate-ai/bioconductor-rtracklayer`
- Raw SKILL.md: https://api.skillmd.com/api/skills/biomate-ai/bioconductor-rtracklayer/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: biomate-ai (https://skillmd.com/u/biomate-ai)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/biomate-ai/bioconductor-rtracklayer

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# rtracklayer

## Dependencies & Environment

> Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.

- **Version:** 1.72.0 · **Bioconductor:** 3.23 · **R:** ≥ 4.6
- **Depends:** GenomicRanges
- **Imports:** XML, BiocGenerics, S4Vectors, IRanges, XVector, Seqinfo, Biostrings, curl, httr, Rsamtools, GenomicAlignments, BiocIO, restfulr
- **System requirements:** URL
- **Install:** `BiocManager::install("rtracklayer")`

## When to Use
- **Genomic Track Import/Export**: Importing and exporting genomic annotation tracks (e.g., BED, GFF, WIG) into R as `GRanges` objects using `import` and `export`.
- **UCSC Genome Browser Interaction**: Interacting programmatically with the UCSC genome browser via `browserSession`.
- **Custom Track Uploads**: Uploading custom annotation tracks to a genome browser using the `track<-` function.
- **UCSC Table Queries**: Querying and downloading built-in UCSC tracks (like RepeatMasker) using `ucscTableQuery` and `getTable`.

## When NOT to Use
- For core manipulation of genomic intervals without file I/O, use `GenomicRanges` instead.
- For parsing raw sequencing alignments, use `GenomicAlignments` or `Rsamtools` instead, as `rtracklayer` is designed for annotation tracks.

## Data Requirements
- **Input Formats**: BED, GFF (v1/2/3), WIG, and other browser-supported formats.
- **R Representation**: Genomic coordinates must be 1-based when represented as `GRanges` in R.
- **Genome Build**: Valid genome build identifiers (e.g., "hg18", "hg19") for UCSC integration.

## Key Parameters
- **format**: Explicitly specifies the file format (e.g., "bed", "gff1") for `import` or `export`.
- **name**: Character vector identifying the track within a `browserSession`.
- **range**: A `GRanges` object specifying the genomic segment to view or download.
- **pack**: Instructs the browser to use the "pack" mode for viewing a track.
- **track**: Specifies the name of the track to query in `ucscTableQuery`.
- **table**: Specifies the specific table within a track to retrieve via `ucscTableQuery`.

## Best Practices
- Use `GRangesForUCSCGenome` to formally associate interval data with a UCSC genome build and validate bounds before uploading.
- Subset large `GRanges` tracks before uploading or viewing (e.g., `targetTrack[1:10]`) to avoid overwhelming the browser session.
- Rely on the default "auto" format detection in `export` and `import` which derives the format from the file extension.

## Common Pitfalls
- **Coordinate System Confusion**: R and `GRanges` use 1-based coordinates, while formats like BED use 0-based. *Fix*: `rtracklayer` handles this automatically during `import`/`export`, so avoid manual coordinate shifting.
- **Opening too many browser tabs**: Changing the view state in UCSC opens a new page in the web browser. *Fix*: Consolidate view adjustments or use `browseGenome` to load tracks and set the view in a single call.

## Alternatives
- **GenomicRanges**: For in-memory manipulation of genomic intervals without external browser interaction.
- **BSgenome**: For retrieving and manipulating full genome sequences rather than annotation tracks.

## Citations
- Lawrence M, et al. (2009) "Software for Computing and Annotating Genomic Ranges." PLoS Computational Biology.
- Lawrence M, et al. (2007) "rtracklayer: an R package for interfacing with genome browsers." Bioinformatics.

## References
- Homepage: https://bioconductor.org/packages/rtracklayer
- Vignette: https://bioconductor.org/packages/release/bioc/vignettes/rtracklayer/inst/doc/rtracklayer.pdf

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## Run this on BioMate

This skill is the **knowledge layer** — when, why, and how to use `rtracklayer`. To **run this analysis on your own data** with managed compute, automated QC, and reproducible outputs, use **[BioMate](https://www.biomate.ai?ref=kb&pkg=rtracklayer)** — free to start.

▶ **[Open `rtracklayer` on BioMate →](https://www.biomate.ai?ref=kb&pkg=rtracklayer)**