Question: Can I add TPM values of Isoforms of the same gene to get total gene expression?
0
gravatar for baunruh
12 months ago by
baunruh0
baunruh0 wrote:

Hello,

If I have TPM values for gene A from the UCSC database which contains multiple isoforms, and lets say I want just 1 output for gene A, can I average or add the TPM values?

If I can't do that is it possible to go back to the raw reads and add them at the raw read level?

I just want to condense genes for my dataset.

sequencing rna-seq next-gen • 531 views
ADD COMMENTlink modified 12 months ago by Michele Busby1.9k • written 12 months ago by baunruh0
2
gravatar for Michele Busby
12 months ago by
Michele Busby1.9k
United States
Michele Busby1.9k wrote:

If they are calculated correctly (e.g. with RSEM or similar), the quantification should be divided among the isoforms in a mutually exclusive way.

So if you have

Isoform1 3 TPM - three transcripts Isoform2 1 TPM - one transcript

The total gene should have 4 transcripts per million (i.e. 4 independent transcripts, 3 from Isoform1 and one from Isoform2.)

ADD COMMENTlink written 12 months ago by Michele Busby1.9k
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