---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
layout: post
title: Data Wrangling - Create a CpG GFF from Pgenerosa_v074 using EMBOSS fuzznuc on Swoose
date: '2019-08-21 12:24'
tags:
  - Panopea generosa
  - GFF
  - fuzznuc
  - EMBOSS
  - geoduck
  - v074
  - Pgenerosa_v074
categories:
  - 2019
  - Geoduck Genome Sequencing
---
Steven wanted me to create a CpG GFF for use in IGV visulations for continued Pgenerosa_v074 analysis. I did that by running the EMBOSS tool `fuzznuc`:

```shell
~/programs/EMBOSS-6.6.0/emboss/fuzznuc \
-sequence ~/data/P_generosa/genomes/Pgenerosa_v074.fa \
-pattern CG \
-outfile 20190821_fuzznuc_pgenv074.gff \
-rformat gff
```

This was run on my computer, `swoose`.

---

# RESULTS

Output folder:

- [20190821_fuzznuc_pgen074/](https://gannet.fish.washington.edu/Atumefaciens/20190821_fuzznuc_pgen074/)

Output GFF:

- [20190821_fuzznuc_pgen074/20190821_fuzznuc_pgenv074.gff](https://gannet.fish.washington.edu/Atumefaciens/20190821_fuzznuc_pgen074/20190821_fuzznuc_pgenv074.gff) (2.4GB)

MD5 checksum:

- f7176f7dfe5e964aa1111cb7013a9f37

This file was also added our [Genomic Resources Wiki](https://github.com/RobertsLab/resources/wiki/Genomic-Resources) (GitHub). The file was renamed to:

- Pgenerosa_v074.CpG.gff
