RepeatMasker on new species

Question

[burnsro]

I have run RepeatMasker on a species of arabidopsis, using a personal library, however in the tbl output it tells me

The query species was assumed to be homo
RepeatMasker version open-4.0.5 , default mode

I cannot change -species command and use a personal library, -lib, at the same time to run RepeatMasker. I am wondering if there is a way to change the default species, or if it is an issue

[nterhoeven]

I am not sure about this, but I belive, this should not be a problem. You could look for some reference transposons (e.g. from TAIR) and check, if your results match these annotated TEs.

Answer 1

[Mehmet]

Hi,

If you want to run RepeatMasker on a new species which is not described on a database, this means that you need to do a do novo mask. for this, before running RepeatMasker, you have to run RepeatModeler which will produce a database for your new species. After RepeatModeler, you can run RepeatMasker easy using output of RepeatModeler. I guess you want to make a soft mask. If yes, please write. I have run these two programs recently. I will be waiting for your answer.

Answer 2

[predeus]

Does anybody know how crucial it is to use your own repeat library in order to successfully mask repeats? I know it would depend on species, of course. Is there much difference in the amount of sequence masked?

Thank you for any input.