Question: Common Cutoff in TPM unit to filter out gene considered as low expressed.
0
gravatar for ZheFrench
2.1 years ago by
ZheFrench210
France
ZheFrench210 wrote:

Question is in the title.

For example you computed "estimated expression" in TPM units per gene for one biological replicate. (with Salmon for example).

In general, what can you admit as a cutoff to remove low expressed genes.

I think I saw 1 was an admited cutoff but not sure. For now I'm filtering by 50th percentile...

rna-seq salmon tpm • 1.4k views
ADD COMMENTlink modified 2.1 years ago by Devon Ryan88k • written 2.1 years ago by ZheFrench210
2
gravatar for Devon Ryan
2.1 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

There's no single cut-off threshold that can be used. You'll need to use a method like zFPKM to determine what's appropriate in your dataset.

ADD COMMENTlink written 2.1 years ago by Devon Ryan88k
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