Does anyone knows if it is OK to analyse small RNA data using Repeatmasker?
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Well, you could, but you wouldn't want to. Am I correct in guessing that you're wondering how much of your small RNA is originating from repeat regions in the genome? -
yes you are correct! I actually would like to know how much TE or piRNA am I getting in my libraries, do you know a better option? that would be nice!Comment
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If you're using a normal model organism for which the genome has already been repeatmasked, then just align to the genome and then count how many of your reads are in the repeat region(s) of interest (it's probably simplest to just count the first alignment in the case of multimappers). Depending on how you align things, you could do that with htseq-count (or presumably featurecounts from subread, though I've never used it) or even GenomicRanges and Rsamtools if you want to get more complicated in how you count things.Comment
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