---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2018-08-28 14:21:16+00:00
layout: post
slug: transposable-element-mapping-crassostrea-virginica-genome-cvirginica_v300-using-repeatmasker-4-07
title: Transposable Element Mapping – Crassostrea virginica Genome, Cvirginica_v300,
using RepeatMasker 4.07
categories:
- 2018
- Miscellaneous
tags:
- Crassostrea virginica
- Eastern oyster
- jupyter notebook
- RepeatMasker
- roadrunner
- TE
- transposable elements
---
Per this [GitHub issue](https://github.com/RobertsLab/resources/issues/352), I'm IDing transposable elements (TEs) in the _Crassostrea virginica_ genome.
Genome used:
* [Cvirginica_v300.fa](https://github.com/RobertsLab/resources/wiki/Genomic-Resources#genome-1)
I ran RepeatMasker (v4.07) with RepBase-20170127 and RMBlast 2.6.0 four times:
1. Species = all
2. Species = _Crassostrea gigas_ (Pacific oyster)
3. Species = _Crassostrea virginica_ (Eastern oyster)
4. Default settings (i.e. no species select - will use human genome).
The idea with running this with four different settings was to get a sense of how the analyses would differ with species specifications.
All runs were performed on roadrunner.
All commands were documented in a Jupyter Notebook (GitHub):
* [20180822_roadrunner_virginica_TEs_repeatmasker.ipynb](https://github.com/RobertsLab/code/blob/master/notebooks/sam/20180822_roadrunner_virginica_TEs_repeatmasker.ipynb)
_NOTE: RepeatMasker writes the desired output files (*.out, *.cat.gz, and *.gff) to the same directory that the genome is located in! If you conduct multiple runs with the same genome in the same directory, it will overwrite those files, as they are named using the genome assembly filename._ Be sure to move files out of the genome directory after each run!
* * *
##### RESULTS:
###### RUN 1 (species - all)
Output folder:
* [20180822_virginica_repeatmasker_all](https://owl.fish.washington.edu/Athaliana/20180822_virginica_repeatmasker_all)
Summary table (text):
* [Cvirginica_v300.fa.tbl](https://owl.fish.washington.edu/Athaliana/20180822_virginica_repeatmasker_all/Cvirginica_v300.fa.tbl)
Output table (GFF):
* [Cvirginica_v300.fa.out.gff](https://owl.fish.washington.edu/Athaliana/20180822_virginica_repeatmasker_all/Cvirginica_v300.fa.out.gff)
##### SUMMARY TABLE
==================================================
file name: Cvirginica_v300.fa
sequences: 11
total length: 684741128 bp (684675328 bp excl N/X-runs)
GC level: 34.83 %
bases masked: 113771462 bp ( 16.62 %)
==================================================
number of length percentage
elements* occupied of sequence
--------------------------------------------------
Retroelements 97003 27946871 bp 4.08 %
SINEs: 48145 9242559 bp 1.35 %
Penelope 1429 256929 bp 0.04 %
LINEs: 27022 10570154 bp 1.54 %
CRE/SLACS 28 2219 bp 0.00 %
L2/CR1/Rex 2160 316660 bp 0.05 %
R1/LOA/Jockey 3058 386611 bp 0.06 %
R2/R4/NeSL 511 226938 bp 0.03 %
RTE/Bov-B 7377 3276312 bp 0.48 %
L1/CIN4 1331 95476 bp 0.01 %
LTR elements: 21836 8134158 bp 1.19 %
BEL/Pao 1807 936488 bp 0.14 %
Ty1/Copia 3046 296183 bp 0.04 %
Gypsy/DIRS1 12789 6060883 bp 0.89 %
Retroviral 2369 152228 bp 0.02 %
DNA transposons 180693 29492426 bp 4.31 %
hobo-Activator 12869 1114188 bp 0.16 %
Tc1-IS630-Pogo 17233 2485049 bp 0.36 %
En-Spm 0 0 bp 0.00 %
MuDR-IS905 0 0 bp 0.00 %
PiggyBac 2388 405926 bp 0.06 %
Tourist/Harbinger 9302 992476 bp 0.14 %
Other (Mirage, 238 15946 bp 0.00 %
P-element, Transib)
Rolling-circles 0 0 bp 0.00 %
Unclassified: 137707 45460608 bp 6.64 %
Total interspersed repeats: 102899905 bp 15.03 %
Small RNA: 45243 9057873 bp 1.32 %
Satellites: 3852 760316 bp 0.11 %
Simple repeats: 203542 8946510 bp 1.31 %
Low complexity: 26205 1281043 bp 0.19 %
==================================================
* most repeats fragmented by insertions or deletions
have been counted as one element
Runs of >=20 X/Ns in query were excluded in % calcs
The query species was assumed to be root
RepeatMasker Combined Database: Dfam_Consensus-20170127, RepBase-20170127
run with rmblastn version 2.6.0+
* * *
###### RUN 2 (species - _Crassostrea gigas_)
Output folder:
* [20180822_virginica_repeatmasker_Cgigas](https://owl.fish.washington.edu/Athaliana/20180822_virginica_repeatmasker_Cgigas)
Summary table (text):
* [Cvirginica_v300.fa.tbl](https://owl.fish.washington.edu/Athaliana/20180822_virginica_repeatmasker_Cgigas/Cvirginica_v300.fa.tbl)
Output table (GFF):
* [Cvirginica_v300.fa.out.gff](https://owl.fish.washington.edu/Athaliana/20180822_virginica_repeatmasker_Cgigas/Cvirginica_v300.fa.out.gff)
##### SUMMARY TABLE
==================================================
file name: Cvirginica_v300.fa
sequences: 11
total length: 684741128 bp (684675328 bp excl N/X-runs)
GC level: 34.83 %
bases masked: 93923386 bp ( 13.72 %)
==================================================
number of length percentage
elements* occupied of sequence
--------------------------------------------------
Retroelements 26397 15008601 bp 2.19 %
SINEs: 4 722 bp 0.00 %
Penelope 675 190160 bp 0.03 %
LINEs: 17645 8922188 bp 1.30 %
CRE/SLACS 0 0 bp 0.00 %
L2/CR1/Rex 70 39188 bp 0.01 %
R1/LOA/Jockey 0 0 bp 0.00 %
R2/R4/NeSL 4 5110 bp 0.00 %
RTE/Bov-B 6194 2718955 bp 0.40 %
L1/CIN4 0 0 bp 0.00 %
LTR elements: 8748 6085691 bp 0.89 %
BEL/Pao 933 788887 bp 0.12 %
Ty1/Copia 47 82743 bp 0.01 %
Gypsy/DIRS1 6819 4822734 bp 0.70 %
Retroviral 0 0 bp 0.00 %
DNA transposons 163945 26422122 bp 3.86 %
hobo-Activator 7742 720623 bp 0.11 %
Tc1-IS630-Pogo 15615 2328538 bp 0.34 %
En-Spm 0 0 bp 0.00 %
MuDR-IS905 0 0 bp 0.00 %
PiggyBac 2246 393498 bp 0.06 %
Tourist/Harbinger 8431 876020 bp 0.13 %
Other (Mirage, 0 0 bp 0.00 %
P-element, Transib)
Rolling-circles 0 0 bp 0.00 %
Unclassified: 160681 41266796 bp 6.03 %
Total interspersed repeats: 82697519 bp 12.08 %
Small RNA: 214 40811 bp 0.01 %
Satellites: 1396 217317 bp 0.03 %
Simple repeats: 216869 9637447 bp 1.41 %
Low complexity: 27520 1418990 bp 0.21 %
==================================================
* most repeats fragmented by insertions or deletions
have been counted as one element
Runs of >=20 X/Ns in query were excluded in % calcs
The query species was assumed to be crassostrea gigas
RepeatMasker Combined Database: Dfam_Consensus-20170127, RepBase-20170127
* * *
###### RUN 3 (species - _Crassostrea virginica_)
Output folder:
* [20180822_virginica_repeatmasker_Cvirginica](https://owl.fish.washington.edu/Athaliana/20180822_virginica_repeatmasker_Cvirginica)
Summary table (text):
* [Cvirginica_v300.fa.tbl](https://owl.fish.washington.edu/Athaliana/20180822_virginica_repeatmasker_Cvirginica/Cvirginica_v300.fa.tbl)
Output table (GFF):
* [Cvirginica_v300.fa.out.gff](https://owl.fish.washington.edu/Athaliana/20180822_virginica_repeatmasker_Cvirginica/Cvirginica_v300.fa.out.gff)
##### SUMMARY TABLE
==================================================
file name: Cvirginica_v300.fa
sequences: 11
total length: 684741128 bp (684675328 bp excl N/X-runs)
GC level: 34.83 %
bases masked: 46637065 bp ( 6.81 %)
==================================================
number of length percentage
elements* occupied of sequence
--------------------------------------------------
Retroelements 43139 8952068 bp 1.31 %
SINEs: 43139 8952068 bp 1.31 %
Penelope 0 0 bp 0.00 %
LINEs: 0 0 bp 0.00 %
CRE/SLACS 0 0 bp 0.00 %
L2/CR1/Rex 0 0 bp 0.00 %
R1/LOA/Jockey 0 0 bp 0.00 %
R2/R4/NeSL 0 0 bp 0.00 %
RTE/Bov-B 0 0 bp 0.00 %
L1/CIN4 0 0 bp 0.00 %
LTR elements: 0 0 bp 0.00 %
BEL/Pao 0 0 bp 0.00 %
Ty1/Copia 0 0 bp 0.00 %
Gypsy/DIRS1 0 0 bp 0.00 %
Retroviral 0 0 bp 0.00 %
DNA transposons 3538 1564942 bp 0.23 %
hobo-Activator 0 0 bp 0.00 %
Tc1-IS630-Pogo 0 0 bp 0.00 %
En-Spm 0 0 bp 0.00 %
MuDR-IS905 0 0 bp 0.00 %
PiggyBac 0 0 bp 0.00 %
Tourist/Harbinger 0 0 bp 0.00 %
Other (Mirage, 0 0 bp 0.00 %
P-element, Transib)
Rolling-circles 0 0 bp 0.00 %
Unclassified: 65151 23982146 bp 3.50 %
Total interspersed repeats: 34499156 bp 5.04 %
Small RNA: 43353 8992879 bp 1.31 %
Satellites: 1 222 bp 0.00 %
Simple repeats: 232627 10544162 bp 1.54 %
Low complexity: 29762 1561018 bp 0.23 %
==================================================
* most repeats fragmented by insertions or deletions
have been counted as one element
Runs of >=20 X/Ns in query were excluded in % calcs
The query species was assumed to be crassostrea virginica
RepeatMasker Combined Database: Dfam_Consensus-20170127, RepBase-20170127
run with rmblastn version 2.6.0+
* * *
###### RUN 4 (default settings - human genome)
Output folder:
* [20180822_virginica_repeatmasker_defaults/](https://owl.fish.washington.edu/Athaliana/20180822_virginica_repeatmasker_defaults/)
Summary table (text):
* [Cvirginica_v300.fa.tbl](https://owl.fish.washington.edu/Athaliana/20180822_virginica_repeatmasker_defaults/Cvirginica_v300.fa.tbl)
Output table (GFF):
* [Cvirginica_v300.fa.out.gff](https://owl.fish.washington.edu/Athaliana/20180822_virginica_repeatmasker_defaults/Cvirginica_v300.fa.out.gff)
##### SUMMARY TABLE
==================================================
file name: Cvirginica_v300.fa
sequences: 11
total length: 684741128 bp (684675328 bp excl N/X-runs)
GC level: 34.83 %
bases masked: 13461422 bp ( 1.97 %)
==================================================
number of length percentage
elements* occupied of sequence
--------------------------------------------------
SINEs: 2056 120820 bp 0.02 %
ALUs 0 0 bp 0.00 %
MIRs 240 14635 bp 0.00 %
LINEs: 3408 331585 bp 0.05 %
LINE1 240 16835 bp 0.00 %
LINE2 728 69177 bp 0.01 %
L3/CR1 1369 135234 bp 0.02 %
LTR elements: 704 236625 bp 0.03 %
ERVL 14 944 bp 0.00 %
ERVL-MaLRs 12 892 bp 0.00 %
ERV_classI 272 36695 bp 0.01 %
ERV_classII 4 206 bp 0.00 %
DNA elements: 1088 100026 bp 0.01 %
hAT-Charlie 27 1543 bp 0.00 %
TcMar-Tigger 142 9891 bp 0.00 %
Unclassified: 57 6096 bp 0.00 %
Total interspersed repeats: 795152 bp 0.12 %
Small RNA: 3698 279669 bp 0.04 %
Satellites: 73 5524 bp 0.00 %
Simple repeats: 247957 10848509 bp 1.58 %
Low complexity: 30084 1536314 bp 0.22 %
==================================================
* most repeats fragmented by insertions or deletions
have been counted as one element
Runs of >=20 X/Ns in query were excluded in % calcs
The query species was assumed to be homo sapiens
RepeatMasker Combined Database: Dfam_Consensus-20170127, RepBase-20170127
run with rmblastn version 2.6.0+
* * *