Hi all,
i am trying to understand the difference between TAU to RPKM.
i know that:
The equation of Tau is :
Ti = Vi/Li X (sigma(Vj/Lj))
Li is the length of isoform i.
Lj is the length of isoform j.
Vi is the fraction of nucleotides. What does it mean?
i also know that:
The equation of RPKM is:
10^9 x (Ci/(NmLi))
Li is the length of isoform i.
Nm is the total number of mappable reads
Ci is the number of reads from isoform i
i know that tau should present the relative abundance(fraction of particular transcript in the transcriptome), and RPKM is a coverage measure.
i am trying to understand the difference by an example:
Suppose there are only three genes (each with a single isoform), A, B, and C.
[Scenario 1]: Suppose that the lengths of the genes are L_A = 12kb, L_B = 4kb, and L_C = 4kb.
[Scenario 2]: Suppose that the lengths of the genes are instead L_A = 4kb, L_B =4kb, and L_C = 12kb.
what should be the RPKM & TAU in those scenarios?
Thanks in advance..
Pap
i am trying to understand the difference between TAU to RPKM.
i know that:
The equation of Tau is :
Ti = Vi/Li X (sigma(Vj/Lj))
Li is the length of isoform i.
Lj is the length of isoform j.
Vi is the fraction of nucleotides. What does it mean?
i also know that:
The equation of RPKM is:
10^9 x (Ci/(NmLi))
Li is the length of isoform i.
Nm is the total number of mappable reads
Ci is the number of reads from isoform i
i know that tau should present the relative abundance(fraction of particular transcript in the transcriptome), and RPKM is a coverage measure.
i am trying to understand the difference by an example:
Suppose there are only three genes (each with a single isoform), A, B, and C.
[Scenario 1]: Suppose that the lengths of the genes are L_A = 12kb, L_B = 4kb, and L_C = 4kb.
[Scenario 2]: Suppose that the lengths of the genes are instead L_A = 4kb, L_B =4kb, and L_C = 12kb.
what should be the RPKM & TAU in those scenarios?
Thanks in advance..
Pap