---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
layout: post
title: Data Wrangling - Olurida_v081 UTR GFFs and Intergenic, Intron BED files
date: '2019-12-14 09:04'
tags:
  - Ostrea lurida
  - Olympia oyster
  - intron
  - UTR
  - Olurida_v081
categories:
  - 2019
  - Miscellaneous
---
After a meeting last week, we realized we needed to update the [paper-oly-mbdbs-gen GitHub repo](https://github.com/sr320/paper-oly-mbdbs-gen/tree/master/genome-features) with the most current versions of feature files we had.

As part of that, we needed a new intron GFF file generated. I also realized that the output from the [MAKER annotation from 20190709](https://robertslab.github.io/sams-notebook/posts/2019/2019-07-09-Genome-Annotation---Olurida_v081-with-MAKER-and-Tissue-specific-Transcriptomes-on-Mox/) actually has 3'/5' UTR features, so I decided to separate those out and create separate GFFs for them, as well.

The process was performed in the following Jupyter Notebook (GitHub):

- [20191214_olur_genome_feature_and_intron_splitting.ipynb](https://github.com/RobertsLab/code/blob/master/notebooks/sam/20191214_olur_genome_feature_and_intron_splitting.ipynb)

One thing to note in that Jupyter Notebook. The `complementBed` command threw an error related to sorting. Two things with this:

1. I don't see an issue with the sorting.

2. It seems to have still run just fine and generated the expected output.

---

# RESULTS

Output folder:

- [20191214_olur_genome_feature_and_intron_splitting/](https://gannet.fish.washington.edu/Atumefaciens/20191214_olur_genome_feature_and_intron_splitting/)


Here's quick glance at IGV visualization of the intron BED file. Things look fine.

![IGV screencap showing Olurida_v081 intron/exon tracks](https://github.com/RobertsLab/sams-notebook/blob/master/images/screencaps/20191214_olur_Olurida_v081_intron_igv.png?raw=true)

The files have been uploaded to the [paper-oly-mbdbs-gen GitHub repo](https://github.com/sr320/paper-oly-mbdbs-gen/tree/master/genome-features), as well as added to our [Genomic Resources wiki](https://github.com/RobertsLab/resources/wiki/Genomic-Resources).
