Cutoff for TPM value
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 ?
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Matteo Schiavinato
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Picasa
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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.
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