I would like to use repeatmasker to identify repetitive element in my de novo assembled genome. I have installed repeatmasker with repbase database in my local server.
My de novo assembled genome is plant fruit crop which is tetraploid crop. It is non-model plant and I don't know which is the nearest clad belong to my genome.
can I use arabidopsis database in repeat masker to find repeats with default settings? Is this correct way to do this?
Below is the running command of repeatmasker
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RepeatMasker my.contigs.fa -species arabidopsis
RepeatMasker version open-4.0.5
Search Engine: Crossmatch [ 1.080812 ]
Master RepeatMasker Database: path/RepeatMaskerLib.embl ( Complete Database: 20140131 )
Building species libraries in: /path/.RepeatMaskerCache/20140131/arabidopsis
- 176 ancestral and ubiquitous sequence(s) for arabidopsis
- 524 lineage specific sequence(s) for arabidopsis
My de novo assembled genome is plant fruit crop which is tetraploid crop. It is non-model plant and I don't know which is the nearest clad belong to my genome.
can I use arabidopsis database in repeat masker to find repeats with default settings? Is this correct way to do this?
Below is the running command of repeatmasker
-----------------------------------------------
RepeatMasker my.contigs.fa -species arabidopsis
RepeatMasker version open-4.0.5
Search Engine: Crossmatch [ 1.080812 ]
Master RepeatMasker Database: path/RepeatMaskerLib.embl ( Complete Database: 20140131 )
Building species libraries in: /path/.RepeatMaskerCache/20140131/arabidopsis
- 176 ancestral and ubiquitous sequence(s) for arabidopsis
- 524 lineage specific sequence(s) for arabidopsis
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