---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
layout: post
title: Genome Annotation - Pgenerosa_v070 and v074 Top 18 Scaffolds Feature Count Comparisons
date: '2019-07-22 11:03'
tags:
  - Panopea generosa
  - geoduck
  - Pgenerosa_v070
  - Pgenerosa_v074
  - v070
  - v074
  - gff
categories:
  - 2019
  - Geoduck Genome Sequencing
---
After [annotating Pgenerosa_v074 on 20190701](https://robertslab.github.io/sams-notebook/posts/2019/2019-07-01-Genome-Annotation---Pgenerosa_v074-MAKER-on-Mox/), we noticed a large discrepancy in the number of transcripts that MAKER identified, compared to Pgenerosa_v070. As a reminder, the Pgenerosa_v074 is a subset of Pgenerosa_v070 containing only the top 18 longest scaffolds. So, we decided to do a quick comparison of the annotations present in these 18 scaffolds Pgenerosa_v070 and Pgenerosa_v074.

Briefly, used `grep` to pull out features identified in the same 18 scaffolds in the Pgenerosa_v074 assembly from [Pgenerosa_v070 annotated GFF from 20190228](https://robertslab.github.io/sams-notebook/posts/2019/2019-02-28-Genome-Annotation---Pgenerosa_v070-MAKER-on-Mox/) and then counted the number of features identified in this newly subsetted GFF. It's all documented in the Jupyter Notebook below.

Jupyter Notebook (GitHub):
- [20190722_swoose_pgen_v070_top18_scaffold_annotation_count.ipynb](https://github.com/RobertsLab/code/blob/master/notebooks/sam/20190722_swoose_pgen_v070_top18_scaffold_annotation_count.ipynb)

---

# RESULTS

Output folder:

- [20190722_pgen_v070_top18_scaffold_annotation_counts/](https://gannet.fish.washington.edu/Atumefaciens/20190722_pgen_v070_top18_scaffold_annotation_counts/)


GFF subset:

- [20190722_pgen_v070_top18_scaffold_annotation_counts/pgen_v070_top18_scaffolds.gff](https://gannet.fish.washington.edu/Atumefaciens/20190722_pgen_v070_top18_scaffold_annotation_counts/pgen_v070_top18_scaffolds.gff)


#### SUMMARY TABLE

| GENOME                    | CDS    | exon   | gene  | mRNA  |
|---------------------------|--------|--------|-------|-------|
| Pgen_v070                 | 169460 | 175006 | 53035 | 53035 |
| Pgen_v070_top18_scaffolds | 41187  | 43554  | 8404  | 8404  |
| Pgen_v074                 | 10764  | 10940  | 1712  | 1712  |


---

Well, we definitely see a difference between annotations of those top 18 scaffolds (~6-fold difference). However, there is still a _huge_ difference between the full Pgenerosa_v070 annotation and the top 18 scaffolds from the Pgenerosa_v070 annotation.

I'll be performing some RNAseq alignments to these various assemblies. That should provide us with some evidence that we can use to support/refute some of the annotations that are present/absent.
