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Does anyone have any experience with the RPKM (reads per kilobase of exon per million mapped reads) as calculated by TopHat? I can't find any documentation on how this is calculated, and I'm trying to make sure that it standardizes for the total number of mapped reads (as suggested by the name of the metric). I would like to compare RPKM values between samples which have different numbers of total reads and mapped reads, and I'm wondering if I need to do my own standardization for the total number of mapped reads or if this is unnecessary because TopHat has already corrected for it.
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Please note that the RPKM calculation was an experimental feature that is now considered deprecated with the release of Cufflinks. I strongly recommend you discontinue using TopHat to calculate it, and move to Cufflinks instead. The RPKM code will be removed from TopHat in the next release.
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