cufflinks-1.0.3 produces very high FPKM values when compared to cufflinks-0.9.3. Why?

pinki999 · 07-29-2011, 01:26 AM

Hi,

The FPKM values produced by the recent cufflinks 1.0.3 are very high when compared to cufflinks-0.9.3. In both the cases I have used -N option. Can anyone tell me whats the reason for this?

Thanks

chenyao · 07-29-2011, 02:20 AM

the same data and the same reference?

pinki999 · 07-29-2011, 02:25 AM

same samples but previously I had mapped to hg18 build but now to hg19 build. I have two groups with 5 biological replicates. When I used cufflinks-0.9.3 before, the FPKM values between the replicates did not vary much. Now with cufflinks-1.0.3 they are varying a lot.

Mark.hz · 09-20-2011, 02:39 PM

I encounter the same problem, with -N too. FPKM is pretty high!

endether · 09-20-2011, 03:10 PM

You may find this link useful: http://cufflinks.cbcb.umd.edu/faq.html#upquart

drdna · 06-09-2012, 07:48 AM

Cufflinks (v2) makes erroneous FPKM calculations. I first suspected this after looking at the alignment files. Now I have fed the program a control dataset (unique genes, no introns) in which the actual abundances of all "transcript reads" are known. As expected, the FPKM values came out too high. With real data, the most extreme example I've found is where cufflinks produced an FPKM of >400, yet there are ZERO reads from the gene in question. User beware...

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07-29-2011, 01:26 AM	#1
pinki999 Member Location: Germany Join Date: Oct 2010 Posts: 37	cufflinks-1.0.3 produces very high FPKM values when compared to cufflinks-0.9.3. Why? Hi, The FPKM values produced by the recent cufflinks 1.0.3 are very high when compared to cufflinks-0.9.3. In both the cases I have used -N option. Can anyone tell me whats the reason for this? Thanks

07-29-2011, 02:20 AM	#2
chenyao Member Location: Beijing Join Date: Jul 2011 Posts: 74	the same data and the same reference?

07-29-2011, 02:25 AM	#3
pinki999 Member Location: Germany Join Date: Oct 2010 Posts: 37	same samples but previously I had mapped to hg18 build but now to hg19 build. I have two groups with 5 biological replicates. When I used cufflinks-0.9.3 before, the FPKM values between the replicates did not vary much. Now with cufflinks-1.0.3 they are varying a lot.

09-20-2011, 02:39 PM	#4
Mark.hz Member Location: Seattle Join Date: Mar 2009 Posts: 18	I encounter the same problem, with -N too. FPKM is pretty high!

09-20-2011, 03:10 PM	#5
endether Member Location: St. Louis Join Date: Feb 2011 Posts: 11	You may find this link useful: http://cufflinks.cbcb.umd.edu/faq.html#upquart

06-09-2012, 07:48 AM	#6
drdna Member Location: Kentucky Join Date: May 2012 Posts: 76	Cufflinks (v2) makes erroneous FPKM calculations. I first suspected this after looking at the alignment files. Now I have fed the program a control dataset (unique genes, no introns) in which the actual abundances of all "transcript reads" are known. As expected, the FPKM values came out too high. With real data, the most extreme example I've found is where cufflinks produced an FPKM of >400, yet there are ZERO reads from the gene in question. User beware...