---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
layout: post
title: Data Wrangling - Renaming, Splitting, and Feature Counts of Updated Pgenerosa_v074 GenSAS Merged GFF
date: '2019-12-03 15:34'
tags:
  - GFF
  - parsing
  - Panopea generosa
  - geoduck
  - genome
  - GenSAS
categories:
  - 2019
  - Geoduck Genome Sequencing
---
In the final GFF from our [GenSAS Pgenerosa_v074.a4 annotation ](https://robertslab.github.io/sams-notebook/posts/2019/2019-09-28-Genome-Annotation---Pgenerosa_v074-a4-Using-GenSAS/), we noticed that there were no repeat motifs/sequences identified on Scaffold 01. The remaining scaffolds all had repeat motifs present on them, so something seemed amiss (see this [GitHub Issue for more info](https://github.com/RobertsLab/resources/issues/788)).

I ended up contacting GenSAS and it turned out there was a bug on their end that led to this issue:


>Taein Lee
>Nov 26, 2019, 7:27 PM (8 days ago)
>to me, jhumann
>
>Hi Sam,
>
>Thank you so much for your report. There was a bug and it has been fixed.
>Your gff3 files has been re-generated.
>
>-Taein
>From: gensas-admin on behalf of sam white
>Sent: Tuesday, November 26, 2019 3:45 PM
>To: gensas-admin; jhumann; taein_lee
>Subject: [Website feedback] Merged GFF missing repeats on only one chromosome
>
>Sam (https://www.gensas.org/user/1671) sent a message using the contact form
>at https://www.gensas.org/gensas-contact.
>
>Hi,
>
>I generated a merged GFF after I "published" my annotation. I included
>RepeatModeler features in the merged GFF.
>
>My genome has 18 chromosomes. All of them except one chromosome (name:
>PGA_scaffold1__77_contigs__length_89643857) has the expected repeats
>annotations present.
>
>I looked at the individual RepeatMasker and RepeatModeler jobs, and both of
>those GFFs identified repeats on PGA_scaffold1__77_contigs__length_89643857.
>
>Would you happen to have any ideas on why
>PGA_scaffold1__77_contigs__length_89643857 isn't showing any repeat features
>in the merged GFF?>
>
>This is for my project Pgenerosa_v074.
>
>Thanks for any insight!
>
>Sam

So, now that I have the updated, final GFF, I want to re-run the GFF splitting into separate feature files, as well as counts and sequence length stats for all features (including repeats).

Everything is documented in this Jupyter Notebook (GitHub):

- [20191203_swoose_pgen_v074.a4_genome_feature_counts.ipynb](https://github.com/RobertsLab/code/blob/master/notebooks/sam/20191203_swoose_pgen_v074.a4_genome_feature_counts.ipynb)

---

# RESULTS

Output folder:

- [20191203_pgen_v074.a4_genome_feature_counts/](https://gannet.fish.washington.edu/Atumefaciens/20191203_pgen_v074.a4_genome_feature_counts/)


I've copied/pasted the summary data for each of the GFFs that were analyzed, for quick reference.

I'll double-check numbers and update the manuscript as needed. Also, all files will be uploaded to the [OSF repository for this paper](https://osf.io/yem8n/files/)

| Feature       | Count   |
|---------------|---------|
| CDS           | 236960  |
| exon          | 236960  |
| gene          | 34947   |
| mRNA          | 38326   |
| repeat_region | 1676544 |
| rRNA          | 8       |
| tRNA          | 16889   |



```
Panopea-generosa-v1.0.a4.gene.gff3
-------------------------
mean       10811.04461
min          166.00000
median      4464.00000
max       283066.00000




Panopea-generosa-v1.0.a4.mRNA.gff3
-------------------------
mean       12903.649559
min          166.000000
median      5453.000000
max       283066.000000




Panopea-generosa-v1.0.a4.tRNA.gff3
-------------------------
mean       74.807745
min        53.000000
median     75.000000
max       314.000000




Panopea-generosa-v1.0.a4.rRNA.gff3
-------------------------
mean      117.125
min       108.000
median    115.000
max       138.000




Panopea-generosa-v1.0.a4.repeat_region.gff3
-------------------------
mean        212.244974
min           6.000000
median      149.000000
max       10981.000000




Panopea-generosa-v1.0.a4.exon.gff3
-------------------------
mean        201.476988
min           3.000000
median      133.000000
max       13221.000000





Panopea-generosa-v1.0.a4.CDS.gff3
-------------------------
mean        201.476988
min           3.000000
median      133.000000
max       13221.000000

Panopea-generosa-v1.0.a4.repeats.LTR.gff3
-------------------------
percent 0.25
sum       2315583.00
mean          711.83
min            11.00
median        323.00
max          6541.00




Panopea-generosa-v1.0.a4.repeats.RC.gff3
-------------------------
percent 0.03
sum       258182.00
mean         429.59
min           13.00
median       464.00
max          674.00




Panopea-generosa-v1.0.a4.repeats.Simple_repeat.gff3
-------------------------
percent 0.55
sum       5138701.00
mean          258.71
min             6.00
median        124.00
max          5981.00




Panopea-generosa-v1.0.a4.repeats.DNA.gff3
-------------------------
percent 1.01
sum       9497156.00
mean          409.48
min            11.00
median        248.00
max          7012.00




Panopea-generosa-v1.0.a4.repeats.SINE.gff3
-------------------------
percent 0.72
sum       6737909.00
mean          156.23
min            11.00
median        165.00
max           934.00




Panopea-generosa-v1.0.a4.repeats.LINE.gff3
-------------------------
percent 3.19
sum       30035624.00
mean           395.53
min             11.00
median         226.00
max           6604.00




Panopea-generosa-v1.0.a4.repeats.Unknown.gff3
-------------------------
percent 32.04
sum       3.018520e+08
mean      1.998300e+02
min       1.100000e+01
median    1.450000e+02
max       1.098100e+04




-------------------------
Repeats composition of genome (percent): 37.79
```