Sam’s Notebook: Transposable Element Mapping – Crassostrea virginica Genome, Cvirginica_v300, using RepeatMasker 4.07


Per this GitHub issue, I’m IDing transposable elements (TEs) in the Crassostrea virginica genome.

Genome used:

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):

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!