---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
layout: post
title: Data Wrangling - Create Pgenerosa_v070 GFFs
date: '2019-05-23 15:23'
tags:
  - Panopea generosa
  - geoduck
  - jupyter
  - GFF
  - Pgenerosa_v070
  - v070
categories:
  - 2019
  - Geoduck Genome Sequencing
---
Since the [MAKER genome annotation of our Pgenerosa_v070 genome assembly](https://robertslab.github.io/sams-notebook/posts/2019/2019-02-28-Genome-Annotation---Pgenerosa_v070-MAKER-on-Mox/) finally completed last week, I decided to separate out the various features into separate GFF files, as I'm sure we'll need/want them at some point. This was all done in a Jupyter Notebook on my computer (swoose) - see notebook linked below.

Created GFF files for:

- [CDS (169,461 features)](http://owl.fish.washington.edu/halfshell/genomic-databank/Pgenerosa_v070.CDS.gff)
- [exons (175,007 features)](http://owl.fish.washington.edu/halfshell/genomic-databank/Pgenerosa_v070.exon.gff)
- [genes (53,036 features)](http://owl.fish.washington.edu/halfshell/genomic-databank/Pgenerosa_v070.gene.gff)
- [mRNAs (53,036 features)](http://owl.fish.washington.edu/halfshell/genomic-databank/Pgenerosa_v070.mRNA.gff)

Files were `rsync`'d to (each one is linked above):

- http://owl.fish.washington.edu/halfshell/genomic-databank

Jupyter Notebook (GitHub):

[20190523_pgen_Pgenerosa_v070_gffs.ipynb](https://github.com/RobertsLab/code/blob/master/notebooks/sam/20190523_pgen_Pgenerosa_v070_gffs.ipynb)

Will add these files to our [Genomic Resources Wiki](https://github.com/RobertsLab/resources/wiki/Genomic-Resources).
