Hi All,

How one can calculate TPM (Transcripts per million) for miRNA tags/reads counts?

eg: 

miRNAids S_1.readcou S_2.readcou
mmu-let-7a-1-3p    421    230
mmu-let-7a-5p    68708    26836
mmu-let-7b-3p    26    7

Thanks,

Manoharan

Hi,

I don't think TPM make sense for miRNA in the sense that TPM for mRNA uses the length. I think you can use edgeR/DESeq2 to normalize and you will get a normalized value that can be compared among samples.

Do you want TPM for some specific reason?

Hi Lorena,

Thanks for your reply,

Do you want TPM for some specific reason?

Yes, To find the novel miRNAs.

I also had the same doubt but I saw this tpm value used in this publication (https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-12-r145 : in Fig 1) for novel miRNA prediction. So I was wondering how did they generate it and I wanted to follow similar pipeline. In this publication the have used TP2M actually.

Regards,

Manoharan