Question: Calculating RPM for miRNA
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gravatar for glady
19 months ago by
glady260
glady260 wrote:

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 • 890 views
ADD COMMENTlink written 19 months ago by glady260

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.

ADD REPLYlink written 19 months ago by ATpoint35k

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?

ADD REPLYlink written 19 months ago by Santosh Anand5.1k
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