Question: Finding gene length
0
gravatar for saj98
2.6 years ago by
saj98100
saj98100 wrote:

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

rna-seq R • 1.1k views
ADD COMMENTlink modified 2.6 years ago by h.mon29k • written 2.6 years ago by saj98100
0
gravatar for h.mon
2.6 years ago by
h.mon29k
Brazil
h.mon29k wrote:

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.

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by h.mon29k

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?

ADD REPLYlink written 2.6 years ago by saj98100

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?

ADD REPLYlink written 2.6 years ago by h.mon29k

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

ADD REPLYlink written 2.6 years ago by saj98100

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

ADD REPLYlink written 2.6 years ago by h.mon29k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1284 users visited in the last hour