Question: Cutoff for TPM value
gravatar for Picasa
10 months ago by
Picasa350 wrote:


I need to filter my transcriptome to speed up some process.

I will map my samples against my transcriptome and compute the TPM value per contig per sample.

Do you have an idea about which minimum TPM value I should use if any sample has it ?

transcriptome tpm • 714 views
ADD COMMENTlink modified 8 months ago by Macspider2.5k • written 10 months ago by Picasa350

Repeat of this question?

ADD REPLYlink written 10 months ago by Satyajeet Khare1.3k
gravatar for Macspider
8 months ago by
Vienna - BOKU
Macspider2.5k wrote:

One of the "established" procedures is the one of taking FPKM=1, and then converting it to TPM by doing:

TPM_threshold = [ 1 / sum(FPKM_sample) ] * 10^6

This would give you a sample-specific TPM threshold which is scaled to the FPKM=1 threshold, used in many publications. However, you should keep in mind that also FPKM=1 was merely a choice.

ADD COMMENTlink written 8 months ago by Macspider2.5k
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