owl/Athaliana/20180523_oly_repeatmasker_pbjelly_sjw_01-01/jelly.out.fasta.preThuMay240214172018.RMoutput

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:

http://onsnetwork.org/kubu4/2018/05/23/transposable-element-mapping-olympia-oyster-genome-assembly-using-repeatmasker-4-07

FILES:

- jelly.out.fasta.cat.gz : Gunzipped file of all RepeatMasker intermediate files. Can be used to quickly re-analyze data with ProcessRepeats command.

- jelly.out.fasta.masked : FastA file of masked contigs.

- jelly.out.fasta.out : Default output table of repeat region identifications; similar to GFF.

- jelly.out.fasta.out.gff : Output table of repeat region identifications in GFF format.

- jelly.out.fasta.tbl : Human-readable summary table of RepeatMasker results.