Cutoff for TPM value

Question

[Picasa]

Hi,

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 ?

[DareDevil]

Your question is answered here

[Satyajeet Khare]

Repeat of this question?

Answer 1

[Matteo Schiavinato]

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.