---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
layout: post
title: Data Wrangling - Pgenerosa_v074.a3 Annotation Genome Feature Sequence Lengths
date: '2019-09-04 15:15'
tags:
  - Panopea generosa
  - geoduck
  - Pgenerosa_v074.a3
  - Panopea-generosa-vv0.74.a3
  - Jupyter
categories:
  - 2019
  - Geoduck Genome Sequencing
---
The [GenSAS Pgenerosa_v074 annotation from 20190710](https://robertslab.github.io/sams-notebook/posts/2019/2019-07-10-Genome-Annotation---Pgenerosa_v074-Using-GenSAS/) (referred to as: Panopea-generosa-vv0.74.a3) recently completed (after nearly a month of running).

In preparation for a paper we're writing, we needed some summary stats for Panopea-generosa-vv0.74.a3. This info will be compiled in to a table for the manuscript. See our Genomic Resources wiki for more info on GFFs:

- [Genomic Resources Wiki](https://github.com/RobertsLab/resources/wiki/Genomic-Resources) (GitHub)

Calculations were performed using Python in a Jupyter Notebook.

Jupyter Notebook (GitHub):

 - [20190904_swoose_pgen_v074.a3_genome_feature_counts.ipynb](https://github.com/RobertsLab/code/blob/master/notebooks/sam/20190904_swoose_pgen_v074.a3_genome_feature_counts.ipynb)

---

# RESULTS

I've copied/pasted the summary data for each of the GFFs that were analyzed, for quick reference. Will get this compiled in to a table of some sort for people to use for the manuscript.

```
Panopea-generosa-vv0.74.a3.exon.gff3
-------------------------
mean        255.932825
min           3.000000
median      157.000000
max       13359.000000




Panopea-generosa-vv0.74.a3.CDS.gff3
-------------------------
mean        255.932825
min           3.000000
median      157.000000
max       13359.000000




Panopea-generosa-vv0.74.a3.mRNA.gff3
-------------------------
mean       13318.053183
min          201.000000
median      2346.000000
max       345225.000000




Panopea-generosa-vv0.74.a3.gene.gff3
-------------------------
mean       13318.053183
min          201.000000
median      2346.000000
max       345225.000000

```
