Question: TPM for miRNA tags
0
gravatar for manoharankumar01
3.1 years ago by
manoharankumar010 wrote:

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 • 852 views
ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by manoharankumar010
Answer: TPM for miRNA tags
0
gravatar for Lorena Pantano
3.1 years ago by
Boston
Lorena Pantano100 wrote:

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?

ADD COMMENTlink written 3.1 years ago by Lorena Pantano100
Answer: TPM for miRNA tags
0
gravatar for manoharankumar01
3.1 years ago by
manoharankumar010 wrote:

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

ADD COMMENTlink written 3.1 years ago by manoharankumar010
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