owl/Athaliana/20180702_oly_repeatmasker_Cgigas Directory contains output files from RepeatMasker for identifying transposable elements in an Olympia oyster genome assembly. Genome assembly used: Olurida_v081 See this page for genome assembly info: https://github.com/RobertsLab/resources/wiki/Genomic-Resources#genome-1 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: http://onsnetwork.org/kubu4/2018/07/03/transposable-element-mapping-olympia-oyster-genome-assembly-olurida_v081-using-repeatmasker-4-07 FILES: - Olurida_v081.fa.cat.gz : Gunzipped file of all RepeatMasker intermediate files. Can be used to quickly re-analyze data with ProcessRepeats command. - Olurida_v081.fa.masked : FastA file of masked contigs. - Olurida_v081.fa.out : Default output table of repeat region identifications; similar to GFF. - Olurida_v081.fa.out.gff : Output table of repeat region identifications in GFF format. - Olurida_v081.fa.tbl : Human-readable summary table of RepeatMasker results.