---
title: "08-gene-files"
output: html_document
---

Getting fasta files from the Genome annotation as opposed to version 5. 
Will use getfasta..


```{bash}
cd ../data
wget --no-check-certificate \
https://gannet.fish.washington.edu/Atumefaciens/20190928_Pgenerosa_v074.a4_gensas_annotation/Panopea-generosa-vv0.74.a4.repeat_region.gff3
```

```{bash}
head ../genome/Panopea-generosa-v1.0.fa
```

```{bash}
head ../data/Panopea-generosa-vv0.74.a4.mRNA.gff3
```




```{bash}
/home/shared/bedtools2/bin/bedtools getfasta \
-fi ../genome/Panopea-generosa-v1.0.fa \
-bed ../data/Panopea-generosa-vv0.74.a4.mRNA.gff3 \
-fo ../analyses/Pg_v0.74.a4.mRNA.fa
```