Cufflinks - Odd MIR FPKM values.

[ramma]

Hi all, I'm getting some odd micro RNA FPKM values in my cufflinks output that I'm trying to troubleshoot. The MIRs will show a large FPKM value in one sample, but a zero FPKM in the other samples which seems incorrect. I did some by eye checks in IGV and can't see why this would be.

Here's an example of what I mean.


The data in IGV doesn't seem to agree with the FPKM values either. Here's MIR3125 viewed in IGV as an Example.

Am I maybe missing a cufflinks or tophat option that would avoid this?

Thanks for any help.

[kenietz]

Hi,
i am sorry to revive that thread but i got the same weird results. In one sample i get FPKM for a transcript and in the other not even tho when i check with IGV i get the same picture as the first sample.

Im using Cufflinks 2.0.2.

Thanks for the help

[SrCardgage]

It's possible the short length of the MIRs is affecting the FPKM calculation. This thread may be relevant:

http://seqanswers.com/forums/showthread.php?t=17638

Most importantly, page down to the explanation by Cole Trapnell (one of the authors of Cufflinks).