txendcutr

Overview

Various mRNA sequencing library preparation methods generate sequencing reads from the transcript ends. Quantification of isoform usage can be improved by using truncated versions of transcriptome annotations when assigning such reads to isoforms. The txendcutr package implements some convenience methods for readily generating such truncated annotations from either their 5’ or 3’ transcript ends and their corresponding sequences.

txendcutr is a standalone fork of txcutr, maintained independently of the upstream Bioconductor package. See Differences from txcutr below for what has changed.

Installation instructions

txendcutr is not published on Bioconductor or CRAN. Install it directly from GitHub. Get the latest stable R release from CRAN, then install txendcutr with:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

## BiocManager::install() also installs from GitHub, and correctly
## resolves this package's Bioconductor dependencies
BiocManager::install("guillermo1996/txendcutr")

or, equivalently, with remotes:

if (!requireNamespace("remotes", quietly = TRUE)) {
    install.packages("remotes")
}

remotes::install_github("guillermo1996/txendcutr")

Example

A typical workflow for txendcutr involves

• loading an existing annotation as a TxDb object
• truncating the annotation from the 3’ or 5’ end
• exporting the truncated annotation (GTF)
• exporting supporting files (FASTA, merge TSV)

library(rtracklayer)
library(txendcutr)
library(BSgenome.Hsapiens.UCSC.hg38)

## load human genome
hg38 <- BSgenome.Hsapiens.UCSC.hg38

## load human GENCODE annotation
txdb <- makeTxDbFromGFF("gencode.v38.annotaton.gtf.gz", organism="Homo sapiens")

## truncate to maximum of 500 nts from the 3' end
txdb_w500 <- truncate3primeTxome(txdb, maxTxLength=500)

## ...or from the 5' end
txdb_5p_w500 <- truncate5primeTxome(txdb, maxTxLength=500)

## export annotation
exportGTF(txdb_w500, file="gencode.v38.txendcutr_w500.gtf.gz")

## export FASTA
exportFASTA(txdb_w500, genome=hg38, file="gencode.v38.txendcutr_w500.fa.gz")

## export merge-table
exportMergeTable(txdb_w500, minDistance=200,
                 file="gencode.v38.txendcutr_w500.merge.tsv.gz")

Differences from txcutr

txendcutr began as a fork of mfansler/txcutr and has since diverged as a standalone package. Key changes:

• Native 5’ truncation. Upstream txcutr only truncates from the 3’ end. txendcutr generalizes truncateTxome() with a txEnd argument ("3prime" or "5prime"), and adds truncate3primeTxome() / truncate5primeTxome() convenience wrappers (each with a quiet option to suppress progress messages).
• Overlap export. truncateTxome() (and both wrappers) accept an overlapFile argument to export a TSV of transcript pairs that were collapsed as duplicates during truncation, for auditing and debugging.
• Faster truncation pipeline. The internal clipping step no longer schedules one BiocParallel task per transcript; transcripts are now batched across workers and processed with a vectorized dplyr pipeline, which is substantially faster on large transcriptomes.

Citation

txendcutr is a derivative work, built directly on the methodology and original implementation of txcutr by Mervin Fansler. If you use txendcutr, please cite both packages.

Below is the citation output from using citation('txendcutr') in R. Please run this yourself to check for any updates on how to cite txendcutr.

print(citation('txendcutr'), bibtex = TRUE)
#> To cite package 'txendcutr' in publications use:
#> 
#>   Rocamora Pérez G, Fansler M (2026). _txendcutr: Transcriptome CUTteR
#>   with 5' and 3' End Support_. R package version 1.0.0,
#>   <https://github.com/guillermo1996/txendcutr>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {txendcutr: Transcriptome CUTteR with 5' and 3' End Support},
#>     author = {Guillermo {Rocamora Pérez} and Mervin Fansler},
#>     year = {2026},
#>     note = {R package version 1.0.0},
#>     url = {https://github.com/guillermo1996/txendcutr},
#>   }

Please also cite the original txcutr package, without which this project would not exist:

#> Fansler M (2025). _txcutr: Transcriptome CUTteR_. R package version
#> 1.15.2, <https://github.com/mfansler/txcutr>.
#> 
#> A BibTeX entry for LaTeX users is
#> @Manual{,
#>   title = {txcutr: Transcriptome CUTteR},
#>   author = {Mervin Fansler},
#>   year = {2025},
#>   note = {R package version 1.15.2},
#>   url = {https://github.com/mfansler/txcutr},
#> }

Note that txendcutr was only made possible thanks to Mervin Fansler’s original work on txcutr, as well as many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.

Code of Conduct

Please note that the txendcutr project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Development tools

• Continuous code testing is possible thanks to GitHub Actions, running on Bioconductor’s Docker containers and BiocCheck, adapted from the workflow originally generated by biocthis for upstream txcutr.
• The documentation is formatted thanks to devtools and roxygen2.
• Unit testing is powered by testthat (3rd edition).

This package originates from Mervin Fansler’s txcutr; see the upstream repository for its own, separately maintained development infrastructure (including a pkgdown documentation site).