Question: RepeatMasker on new species
gravatar for burnsro
5.5 years ago by
burnsro20 wrote:

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

transposons • 2.2k views
ADD COMMENTlink modified 18 months ago by predeus1.4k • written 5.5 years ago by burnsro20

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.

ADD REPLYlink written 5.5 years ago by nterhoeven120
gravatar for Mehmet
5.5 years ago by
Mehmet660 wrote:


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.

ADD COMMENTlink written 5.5 years ago by Mehmet660
gravatar for predeus
18 months ago by
predeus1.4k wrote:

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.

ADD COMMENTlink written 18 months ago by predeus1.4k
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