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comprna / SUPPA

SUPPA: Fast quantification of splicing and differential splicing
MIT License
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"Differential transcript usage", the cognate gene expression? #188

Open iamhealthy opened 3 months ago

iamhealthy commented 3 months ago

Hi,

My interest is "differenctial transcript usage".

My question is: How could I obtain differential gene (not transcript) expression? Using (the formatted) iso_tpm file? Then I could analyze the differential transcripts and genes together. Could you please give me some tips?

Many thanks!

EduEyras commented 3 months ago

Please have a look at tximport: https://github.com/thelovelab/tximport to summarise the transcript quantification per gene to perform differential gene expression Best Eduardo

On Fri, 5 Apr 2024 at 22:49, iamhealthy @.***> wrote:

Hi,

My interest is "differenctial transcript usage".

My question is: How could I obtain differential gene (not transcript) expression? Using (the formatted) iso_tpm file? Then I could analyze the differential transcripts and genes together. Could you please give me some tips?

Many thanks!

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