https://github.com/poisonalien/gtf2fasta

Tookit for gtf format conversion and sequence extraction
https://github.com/poisonalien/gtf2fasta

gtf rna-seq

Last synced: 6 months ago
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Tookit for gtf format conversion and sequence extraction

• Host: GitHub
• URL: https://github.com/poisonalien/gtf2fasta
• Owner: PoisonAlien
• License: mit
• Created: 2017-04-17T09:52:04.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2024-01-26T14:55:06.000Z (over 1 year ago)
• Last Synced: 2025-04-30T10:49:02.958Z (6 months ago)
• Topics: gtf, rna-seq
• Language: Julia
• Size: 10.7 KB
• Stars: 5
• Watchers: 2
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# gtf2fasta

A minimal tool for sequence extraction for every transcript (only from exonic regions) in a [gtf](http://mblab.wustl.edu/GTF22.html) from a fasta file. 

It's written in [Julia](https://julialang.org/) and has no dependencies. See [here](https://julialang.org/downloads/) for Julia installation.

This tool requires [indexed fasta file](http://www.htslib.org/doc/faidx.html) for memory efficient sequence extraction.

## Usage

```bash

#Extracting fasta sequence from gtf file (sequences are written to stdout)

$ gtf2fasta.jl ens82.gtf hg19.fa | head

>ENST00000456328

GTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCA

GACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCA

GGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTG

...

```

It will also generate `ens82.gtf.transcript.dict.tsv` with transcript to gene mappings.