A question for calculating the FPKM or TPM for exons

Dear all, I am recently dealing with some RNA-seq data and want to calculate the PSI value for every exon to study alternative splicing, I need to calculate the TPM or FPKM for every exon and I want to know if there are some scripts or software can do it?

fpkm tpm exon

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written 4.0 years ago by pxd •

1 answer

The formulas are fairl simple:

FPKM  =  COUNT / (LENGTH / 10^3 * TOTAL _MAPPED / 10^6)

see more here

https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/

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written 4.0 years ago by Istvan Albert

Thank a lot for your help and I will try to write the script using the functions for them and try to solve.

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written 4.0 years ago by pxd •

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