owl/Athaliana/20180523_oly_repeatmasker_pbjelly_sjw_01-01 Directory contains output files from RepeatMasker for identifying transposable elements in an Olympia oyster genome assembly. Genome assembly used: pbjelly_sjw_01 See this page for genome assembly info: https://github.com/RobertsLab/project-olympia.oyster-genomic/wiki/Genome-Assemblies RepeatMasker was run with default options and the following changes: - ```-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: FILES: - stderr.err : Text file containing standard error output. - stdout.out : Text file containing standard out output.