relationship between relative abundance and relative activity

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6.1 years ago

bitpir ▴ 250

Hello, I have a bunch of meta-transcriptomics data and I would like to identify which organism is the most active. I plan to calculate TPM/RPKM for each organism and the figure out the "most-active" organism that way. However, I find that this method is over-simplified as I am not taking into account the relative abundance (genome copy number) into my calculation, right? If so, what's the best way to calculate relative activity from meta-trancriptomic data then?

Thank you so much for your help!

meta-transcriptomics RNA-seq • 1.0k views

ADD COMMENT • link updated 5.9 years ago by Biostar 20 • written 6.1 years ago by bitpir ▴ 250

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First you should clearly define/explain what "most active" is. Is this referring to a specific gene? Or rather which organism is most abundant in the metasample?

ADD REPLY • link 6.1 years ago by ATpoint 86k

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I think that is something I am struggling with too. I think what I want to get at is to figure out which organism is transcribing the most, i.e most viable?

ADD REPLY • link 6.1 years ago by bitpir ▴ 250

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