Filtering repetitive element during mapping
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?
1 answer
The UCSC Genome Browser provides the genome with repeats masked in this file http://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/chromFaMasked.tar.gz
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