---
title: "19-get-gene-annotations"
output: html_document
date: "2024-09-26"
---
Rmd to get gene annotation lists from augustus.hints.gtf


```{bash}
pwd
```



Use code from Sam White from this GitHub Issue: [1965](https://github.com/RobertsLab/resources/issues/1965) 
```{bash}
awk '$3 == "gene"' ../data/augustus.hints.gtf > ../data/gene_annotation.tab
```

check new file:
```{r}
geneannot <- read.table("../data/gene_annotation.tab")
head(geneannot)
```
looks good! push to repo. 


`join` the table with the `hisat2` count matrices. 