TPM for miRNA tags
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@manoharankumar01-9971
Last seen 7.1 years ago

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

mirna • 2.0k views
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@lorena-pantano-6001
Last seen 3.9 years ago
Boston

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?

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@manoharankumar01-9971
Last seen 7.1 years ago

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

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