Is it good to merge transcripts tpm to gene which is of different gene type?

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4.1 years ago

newbie ▴ 130

I have gene expression data from kallisto with tpm expression. I would like to sum the tpm of transcripts that belong to the same gene and just summarize the TPMs for each gene.

But I see that same gene has a different gene_type. In that case can I sum the tpm of transcripts that belong to the gene? Do you think this can be done or not possible?

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RNA-Seq kallisto tpm • 2.1k views

ADD COMMENT • link updated 4.1 years ago by wensulin93 • 0 • written 4.1 years ago by newbie ▴ 130

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Yea, usually we use tximport or tximeta to get the gene-level values

ADD REPLY • link 4.1 years ago by darklings ▴ 580

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I would like to sum the tpm of transcripts that belong to the same gene and just summarize the TPMs for each gene.

You probably should state what your goal is.

I would also suggest having a look at guidelines such as https://www.bioconductor.org/help/course-materials/2019/CSAMA/materials/labs/lab-03-rnaseq/rnaseqGene_CSAMA2019.html

ADD REPLY • link 4.1 years ago by WouterDeCoster 47k

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My goal is to use the genes tpm for estimating immune cell infiltration. For this I have to use Gene names and their tpm.

ADD REPLY • link 4.1 years ago by newbie ▴ 130

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I think gene part mutation is very normal in genome. If the similarity still remains very high, I think it is not a matter.

ADD REPLY • link 4.1 years ago by wensulin93 • 0

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Are you sure this answer is relevant to the question here? What do mutations have to do with this and where is similarity assessed?

ADD REPLY • link 4.1 years ago by WouterDeCoster 47k

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