I need a tool to analyze the reference sequence, especially about the repeats in it.
Is MUMmer enough?
Thank you for your help!
Is MUMmer enough?
Thank you for your help!
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If by "analyze" you mean "find" then I would recommend TRF by Gary Benson's lab. If by "analyze" you mean "infer alleles from nextgen data" then the answer is more complicated. -
But it seems that TRF only gives me the tandem repeats.Originally posted by genericforms View Post
I need the information about the sparsed repeats, too.
Thank you!Comment
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So for the most comprehensive list of repetitive regions I would go for RepeatMasker. Fortunately UCSC hosts RepeatMasker runs so depending on the reference genome you might not even have to run anything.Originally posted by ufwsse View PostComment
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