owl/Athaliana/20180529_virginica_repeatmasker

Directory contains output files from RepeatMasker for identifying transposable elements in an Crassotrea virginica NCBI genome assembly.

Genome assembly used: GCF_002022765.2_C_virginica-3.0_genomic.fasta

See the NCBI page for genome assembly info:

ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/022/765/GCA_002022765.4_C_virginica-3.0

RepeatMasker was run with default options and the following changes:

- -species "crassostrea virginica" : Set RepBase species to Crassostrea virginica

- -par 15 : Use 15 CPU threads

- -gff : Create GFF output file (in addition to default files)

- -excln : Adjusts output table calculations to exclude sequence runs of >=25Ns. Useful for draft genome assemblies.

- 1> : Send stdout to file instead of printing to notebook.

- 2> : Send stderr to file instead of printing to notebook.


See my notebook for more details:

 http://onsnetwork.org/kubu4/2018/05/29/transposable-element-mapping-crassostrea-virginica-ncbi-genome-assembly-using-repeatmasker-4-07

FILES:

- GCF_002022765.2_C_virginica-3.0_genomic.fasta : C.virginica genome assembly downloaded from NCBI.

- GCF_002022765.2_C_virginica-3.0_genomic.fasta.cat.gz : Gunzipped file of all RepeatMasker intermediate files. Can be used to quickly re-analyze data with ProcessRepeats command.

- GCF_002022765.2_C_virginica-3.0_genomic.fasta.masked : FastA file of masked contigs.

- GCF_002022765.2_C_virginica-3.0_genomic.fasta.out : Default output table of repeat region identifications; similar to GFF.

- GCF_002022765.2_C_virginica-3.0_genomic.fasta.out.gff : Output table of repeat region identifications in GFF format.

- GCF_002022765.2_C_virginica-3.0_genomic.fasta.tbl : Human-readable summary table of RepeatMasker results.

- rm_stderr.err : Standard error from RepeatMasker.

- rm_stdout.out : Standard output from RepeatMasker.

- wget_stderr.txt : Standard error from wget command used to download genome assembly from NCBI.

- wget_stdout.txt : Standard output from wget command used to download genome assembly from NCBI.