Filtering repetitive element during mapping

Question

[dahun73]

Hello,

I have a question for mapping. I want to align mm10 genome without any repetitive element but it is hard to get a repetitive element sequence. RepBase is not free to use for individual user. Is there any good suggestion for mapping without repetitive element?

Answer 1

[JC]

The UCSC Genome Browser provides the genome with repeats masked in this file http://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/chromFaMasked.tar.gz

[dahun73]

I'm sorry for late reply. Thanks! I will check it now!