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Old 11-10-2012, 09:14 AM   #1
zarthon59
Junior Member
 
Location: Montreal

Join Date: Apr 2012
Posts: 3
Default isoform lengths to gene length

Hello everybody,

I was wondering if it was possible, from a list of its isoform lengths to calculate the gene length. I know RSEM is doing it, but I wouldn't want to run another pipeline...
Here is the deal :

length
isoform1 994
isoform2 1723
isoform3 2214

RSEM gives, from these 3 isoforms:

length
gene 1714.64

I have already organized lists of isoforms. So it is pretty easy to gather them together into genes. I did that to get gene abundances from the isoforms abundance, but I am stuck with the gene lengths. Is there an easy way of calculating it?

here is what I found on the web :
"The classic way as defined in [MWM+08] takes the number of bases that
is covered by at least one isoform of that gene. Alternatively, the average isoform length of a gene can be used. As a third option, the RSEM read assignment on isoform level can be used to calculate the gene length as a weighted average of isoform length."

Thanks!!
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