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Dfam-consortium / RepeatMasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
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Is RepeatMasker applicable to RNA-seq data（paired or single）? #180

Closed wutaotao185 closed 2 years ago

wutaotao185 commented 2 years ago

Hello！

Firstly，it's a imporant software truly, thanks for your creation. Then, i have some questions about RepeatMasker. I read many introductions about this software and find that genome file(fasta) is the input file.

I have two questions:

  1. Is the genome file in introduction the result of DNA-seq?
  2. Is RepeatMasker applicable to RNA-seq data?

I have many RNA-seq datas as follows: 1663839630199

I would be very grateful if you can explain more in detail.

Thanks!

Best,

Wu

rmhubley commented 2 years ago

Hi Wu,

The input file is assumed to be nucleotide sequences as the libraries used for comparison are DNA sequences. Further the code has never been tested using custom RNA sequence libraries although I imagine only slight modifications would be necessary to support that functionality.

-R