Skip to content

UCSC-Treehouse/transcript2genome_coords

Repository files navigation

transcript2genome_coords

This script translates coordinates from transcript space to genome space, requiring only a minimal gtf. It is more flexible about the input format than transcriptToGenome in the ensembldb R package, which requires ensembl-specific entries in the gtf.

We developed this script while working on a project that required translating coordinates from FLAIR-generated sample-specific transcripts back to the hg38 genome.

It takes less than 1 minute to translate 100,000 coordinates using a gene model with 15,000 transcripts.

The file names are hard-coded; anyone who wants to make the code more robust is welcome to clone the repo. Pull requests are welcome.

About

No description, website, or topics provided.

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published