Calculating RPM for miRNA
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5.3 years ago
glady ▴ 320

Hello, While calculating RPM the read counts should be divided by : total number of MAPPED READS from a given library or by the total number of reads in the sample ?

Thank you.

RNA-Seq • 2.8k views
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It should be the total number of reads assigned to your list of miRNAs. In a count matrix where columns are samples and rows are genes (or here miRNAs), the total read number per sample would be the column sum.

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Mapped reads, because that is what ultimately defines the depth at which a gene or any genomic element has been sequenced. BTW, use TPM instead of RPKM / FPKM, as the latter does not allow to compare between the samples: C: Which normalization method to use FPKM/TPM?

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