RPM(CPM)RPKMFPKMTPM

更新时间:2023-07-30 14:49:57 阅读: 评论:0

RPM(CPM)RPKMFPKMTPM RPM/RPKM/FPKM/TPM是我们在定义表达量时常⽤的⼏种计算⽅式,那么究竟有什么区别呢?
RPM/CPM
RPM/CPM: Reads/Counts of exon model per million mapped reads
Calculate Formula:
RPM=Total exon reads/ Mapped reads(Millions)
We can get the decision easily: The longer the gene, the greater the number of reads.
So, we calculate the RPKM to exclude the effect of gene length
RPKM
RPKM: Reads Per Kiloba of exon model per Million mapped reads
Range of U: Single-end RNA-q
Calculate Formula:
RPKM=Total exon reads/[Mapped reads(Millions)*Exon length(Kb)]
Example of Calculating RPKM
issn代表什么Gene B is twice as long as gene A, and that might explain why it always gets twice as many reads, regardless of replicate. Sample3 has way more reads than other replicates, regardless of the gene.
RPKM-Step1:normalize for Read Depth
For the purpo of this 4 gene examples, we’re scaling the total read counts by 10 instead of 1,000,000.
Originally,1,000,000 was picked just becau it made the numbers look nice.(i.e. they didn’t require too many decimal places)
RPM-scaled using the ‘per million’ factors.
麦克格雷迪
RPKM-Step2:normalize for gene length
竹馆里>包你说Reads are scaled for depth(M) and gene length(K).
FPKM
数学广角
RPKM and FPKM-two very cloly related terms
RPKM=Reads Per Kiloba Million
FPKM=Fragments per Kiloba Million
RPKM is for single-end RNA-q.
FPKM is for paired-end RNA-q.
Differences
十二生肖年龄
针对Single-end RPKM与FPKM基本没有差异
针对Paired-end,如果⼀对paired-read都⽐对上那么FPKM计算⽅法中认为这⼀对read为⼀个fragment(RPKM则计为2),如果⼀对中仅有⼀个⽐对上,则将⽐对上的计为⼀个fragment.
TPM
TPM is like RPKM and FPKM, except the order of operation is switched.
因此⽐对TPM和FPKM的公式可以发现,FPKM的分母没有考虑基因长度的影响,所以TPM更加符合我们对相对表达量的定义。
Example of Calculating TPM颜字组词
蜂糖TPM-Step1:Normalize for gene length
RPK-scaled by gene length
TPM-Step2:normalize for quencing depth
TPM-scaled by gene length and quencing depth(M)
RPKM vs TPM
With TPM, everyone gets the same sized pie

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