Question: RepeatModeler and RepeatMasker for non-model species
gravatar for nancydong20
3.4 years ago by
nancydong20100 wrote:

Hello everyone!

I am trying to analyze repeat elements in a new draft genome of a non-model organism. I used RepeatModeler to build a de novo repeat library, and then used RepeatMasker (rmblastn version 2.2.27+) to mask the genome. In the .tbl output, I see that no simple repeats or low complexity regions were annotated and many of the subfamilies of SINEs and LINEs are 0%.

An image of the output can be see here:

The commands I used were:

> BuildDatabase -name Reference -engine ncbi ref.fa
> RepeatModeler -engine ncbi -database Reference  
> RepeatMasker -s -lib ~/consensi.fa.classified -dir ~/my_RM_output_dir_Aug11 -e ncbi ~/database/LS_genome.fa

If this is useful in anyway, the query species was assumed to be fly and the analysis used the RepeatMasker Combined Database: Dfam_Consensus-20170127, RepBase-20170127.

What could be the reason that many of the results are coming back as 0%?

Thank you very much!

repeatmodeler repeatmasker • 4.0k views
ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by nancydong20100

Did u solve ur problem.? because i'm also getting something similar to ur result.

ADD REPLYlink written 14 months ago by ashaneev0720
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