---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
layout: post
title: Data Wrangling - Create Panopea-generosa-vv0.74.a4 Intron and Intergenic BED Files
date: '2019-10-30 08:46'
tags:
  - Panopea generosa
  - Panopea-generosa-vv0.74.a4
  - BED
  - intron
  - intergenic
categories:
  - 2019
  - Geoduck Genome Sequencing
---
Since generating an [updated Pgenerosa_v074 annotation](https://robertslab.github.io/sams-notebook/posts/2019/2019-09-28-Genome-Annotation---Pgenerosa_v074-a4-Using-GenSAS/), we also needed updated intergenic and intron bed files to put in the [OSF repository for this project](https://osf.io/yem8n/).

I generated intergenic and intron BED files by following along with Steven's notebooks:

Steven intergenic BED file notebook (GitHub):

- [30-Creating-intragenic-track.ipynb](https://github.com/sr320/nb-2019/blob/master/P_generosa/30-Creating-intragenic-track.ipynb)

Steven intron BED file notebook (GitHub):

- [24-Creating-intron-track.ipynb](https://github.com/sr320/nb-2019/blob/master/P_generosa/24-Creating-intron-track.ipynb)


Here's how I generated these two BED files.

Jupyter Notebook (GitHub):

- [20191030_swoose_pgen_v074.a4_intron_intergenic_features.ipynb](https://github.com/RobertsLab/code/blob/master/notebooks/sam/20191030_swoose_pgen_v074.a4_intron_intergenic_features.ipynb)

---

# RESULTS

Output folder:

- [20191030_pgen_v074.a4_intron_intergenic_features/](https://gannet.fish.washington.edu/Atumefaciens/20191030_pgen_v074.a4_intron_intergenic_features/)

Intergenic BED file (BED):

- [Panopea-generosa-vv0.74.a4.intergenic.bed](https://gannet.fish.washington.edu/Atumefaciens/20191030_pgen_v074.a4_intron_intergenic_features/Panopea-generosa-vv0.74.a4.intergenic.bed)

Intron BED file (BED):

- [Panopea-generosa-vv0.74.a4.introns.bed](https://gannet.fish.washington.edu/Atumefaciens/20191030_pgen_v074.a4_intron_intergenic_features/Panopea-generosa-vv0.74.a4.introns.bed)


Will add these files to the [OSF repository for this project](https://osf.io/yem8n/).

Here's how they look in IGV:

![IGV screencap showing intron and intergenic bed files](https://github.com/RobertsLab/sams-notebook/blob/master/images/screencaps/20191030_pgen_Panopea-generosa-vv0.74.a4_intron-intergenic_igv.png?raw=true)
