/gannet/Atumefaciens/20190327_cgig_repeatmasker_all

Generate transposable element mapping of Crassostrea gigas genome using RepeatMasker.

Used the following genome as input:

http://owl.fish.washington.edu/halfshell/genomic-databank/Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa

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FILES

- Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa.cat.gz: Gzip file of RepeatMasker repeat mapping output.

- Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa.masked: FastA file with all repeats masked.

- Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa.out: Tab-delimited table of RepeatMasker results for each repeat identified.

- Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa.out.gff: GFF file of repeats.

- Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa.tbl: RepeatMasker summary table of repeat results. Human-readable.

- stderr.err: Standard error log.

- stdout.out: Standard out log.



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Notebook:

https://robertslab.github.io/sams-notebook/2019/03/27/Transposable-Element-Mapping-Crassostrea-gigas-Genome-v9-Using-RepeatMasker-4.07-on-Roadrunner.html