I want to perform repeatmasking on ant genome. Ant is also included in the repeat library obtained from Repbase. The library RepeatMaskerLib.embl also contains my species. However, I also generated de novo repeat library by repeatmodeler (consensi.fa). How can I use both libraries for masking ant genome? Should I concatenate RepeatMaskerLib.embl and consensi.fa or can I use both library with single command?
The lib file used by RepeatMasker is simply a variant on the fasta theme. So long as you have a hash (#) in the fasta header, preferably with some repeat family classification but you can make them all unknown, then it should work. You can concatenate entries from as many sources as you have available: Repbase, repeatmodeler, entries from ENA or from the literature.
Finally, if this is a sequenced genome with a genomic database see if you can source their lib file as well. RepeatMasker can handle redundancy in the lib file, though obviously this can make analysis of the results harder.
The lib file used by RepeatMasker is simply a variant on the fasta theme. So long as you have a hash (#) in the fasta header, preferably with some repeat family classification but you can make them all unknown, then it should work. You can concatenate entries from as many sources as you have available: Repbase, repeatmodeler, entries from ENA or from the literature.
Finally, if this is a sequenced genome with a genomic database see if you can source their lib file as well. RepeatMasker can handle redundancy in the lib file, though obviously this can make analysis of the results harder.
Kindly am having a similar issue, I have obtained libraries using denovo ( structure method), I combined them into one file obtained libraries.fa,
Furthermore, I excute
repeatmasker -lib obtainedlibraries.fa genome.fa
But unfortunately repeatmasker return with 0 annotations .tbl, but masking and genome coverage I assume accurately .
Subsequently, in repeatmasker documentation mentioned the library must be in a specific format, I have tried using smaller combinedlibrary.fa lib with edited header according to the information and I have succeeded but not accurately able to detect class but not subclass sometimes
My question, is their any script or tool can edit the repeat header format to suet repeat masker tool
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