Question: (Closed) How to convert TPM to raw reads
0
gravatar for Ashley
19 months ago by
Ashley40
China
Ashley40 wrote:

How to convert TPM to raw reads data:

tf_symbol       11327-117E4     11376-118A8
ADNP    32.9714806792   18.3495163063
ADNP2   3.21150785836   3.27021082687
AEBP1   148.799864104   123.359619525
AEBP2   12.8460314335   7.9938486879
AFF1    56.5225383072   45.7829515762
AFF2    0.428201047782  0.363356758541
AFF3    0.428201047782  0.545035137812
AFF4    52.0264273055   50.8699461958
AHCTF1  20.3395497696   18.7128730649

(values indicate TPMs for each gene;the column indicates samples and the row indicates genes)

ADD COMMENTlink modified 19 months ago by Devon Ryan87k • written 19 months ago by Ashley40

Hello Ashley!

We believe that this post does not fit the main topic of this site.

It is unclear what you are asking, what have you tried? The post body is in no way helpful in determining what is being asked.

Please improve your question, providing reproducible examples of the data and code used. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink modified 19 months ago • written 19 months ago by Michael Dondrup45k

Thanks, got it. Thank you very much! I'll follow your advice.

ADD REPLYlink written 19 months ago by Ashley40

Please edit your question, once it is improved, I will re-open it.

ADD REPLYlink written 19 months ago by Michael Dondrup45k

for TPM you divide (among other things) by the total number of reads. This info is lost. In addition to this you also normalize by something like 'effective exon length' and you would need to know how the person/program actually calculated this, which reference was used etc. This will not work.

Start again from raw data.

ADD REPLYlink written 19 months ago by Ido Tamir4.9k

That's very helpful for me! Thank you very very much!

ADD REPLYlink written 19 months ago by Ashley40
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