Gene Selection GTex for DESeq2 Analysis
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Bine • 0
@bine-23912
Last seen 2 days ago

Dear all,

Not sure if I can ask this question here, please remove it if it is not allowed.

Does anyone know what is exactly meant by "> 6 reads" in below information published on the GTEx website:

"Genes were selected based on expression thresholds of >0.1 TPM in at least 20% of samples and ≥6 reads in at least 20% of samples". https://gtexportal.org/home/documentationPage

I understand what is meant with 0.1 TPM in at least 20% of samples but 6 reads in 20% of samples, I dont quite get the difference between TPM and reads I think.

Thank you, Bine

DESeq2 GTEx • 56 views
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@mikelove
Last seen 2 days ago
United States

TPM and sequenced reads are different. TPM is an estimate of the abundance, where read counts are literally just the count of reads that were assigned (uniquely or probabilistic) to a feature in a sample. Try reading about TPM vs read counts with Google, you'll find lots of online material.

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Thank you for clarifying, will read more about it then. Maybe the read counts are the "raw reads"?

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