Finding gene length

Question

[saj98]

Hello everyone

I have RNA seq data and I would like to find gene length. I used Tophat and Bowtie to get cufflinks. Any idea about how to count gene length.

Thanks for help

Answer 1

[h.mon]

EDIT: here is the answer to what the OP really wants to do.

This page has a simple formula to convert FPKM to TPM. You may use the R function fpkmToTpm() to perform the conversion, available at this repository. The function is so short I can copy it here:

fpkmToTpm <- function(x)
{
    lDenom <- log(sum(x))
    exp(log(x) - lDenom + log(1e6))
}

Old answer: See "Output formats used in the Cufflinks suite", some output files include transcript length.

P.S.: and please rewrite your question to make it more clear.

[saj98]

my question How I can get gene length? I am looking for gene length to calculate TPM value instead of FPKM value. Is that clear?

[h.mon]

More or less clear what you want, totally unclear what you did so far. Did you run cufflinks? How did you run cufflinks? Did you see cufflinks outputs transcript length?

[saj98]

Here is what I got from cuufflinks:

setwd("D:/PHD thesisi/diff_out") cuff <- readCufflinks() cuff CuffSet instance with: 2 samples 55004 genes 94479 isoforms 72846 TSS 27521 CDS 55004 promoters 72846 splicing 21901 relCDS Thanks for your help and sorry for confusing

[h.mon]

See my updated answer, you do not need the gene lengths for the conversion.