Hello Wen,

It's not necessary to send multiple emails to the mailing list; we track incoming emails to ensure that we respond to all of them.

Your FPKM values do look high, but keep in mind that coverage is only part of the FPKM calculation; it's also dependent on transcript length and the total number of reads in your sample. Your transcript lengths look very short, so that may be skewing your FPKM values. For the record, Cufflinks is using scientific/E notation, so e denotes powers of 10 in the FPKM output. 

A good place to ask followup questions about cufflinks output is the cufflinks help email address: tophat.cufflinks@gmail.com

Good luck,
J.

On Jun 24, 2011, at 10:35 AM, Wen Huang wrote:

Dear Galaxy team and users,

I have a question on the output by cufflinks on Galaxy.

I started with about 28M paired-end reads and mapped them to the reference genome using Tophat on Galaxy. The aligned fragments were assembled by cufflinks, again on Galaxy and I got an output with the first few lines on the bottom of this email.

I was wondering how could cufflinks possibly estimate FPKM on the order of e+07 when the coverage is between 8-50 fragments per base and the total mapped fragments smaller than 28M. Assuming that 20M fragments were mapped, the FPKM should be something around coverage/28. Was the e in the output the Euler's number or 10?

I appreciate your help.

Thanks,
Wen Huang
tracking_id	class_code	nearest_ref_id	gene_id	gene_short_name	tss_id	locus	length	coverage	status	FPKM	FPKM_conf_lo	FPKM_conf_hi
CUFF.2.1	-	-	CUFF.2	-	-	chr1:90301-90706	405	21.1837	OK	1.84527e+07	1.10716e+07	2.58338e+07
CUFF.1.1	-	-	CUFF.1	-	-	chr1:65419-65692	273	30.9833	OK	2.31848e+07	8.52143e+06	3.78481e+07
CUFF.3.1	-	-	CUFF.3	-	-	chr1:135255-135896	641	8.61389	OK	6.31907e+06	3.41968e+06	9.21846e+06
CUFF.4.1	-	-	CUFF.4	-	-	chr1:155808-156529	721	7.26147	OK	5.32695e+06	2.88278e+06	7.77112e+06
CUFF.5.1	-	-	CUFF.5	-	-	chr1:160421-160729	308	17.6004	OK	1.77483e+07	7.50132e+06	2.79953e+07
CUFF.6.1	-	-	CUFF.6	-	-	chr1:170695-171212	517	9.16414	OK	8.41605e+06	4.44869e+06	1.23834e+07
CUFF.7.1	-	-	CUFF.7	-	-	chr1:180885-181188	303	30.5702	OK	2.6515e+07	1.36533e+07	3.93767e+07
CUFF.8.1	-	-	CUFF.8	-	-	chr1:184397-184702	305	26.712	OK	2.13696e+07	9.94707e+06	3.27921e+07
CUFF.10.1	-	-	CUFF.10	-	-	chr1:233237-234095	858	3.71208	OK	3.31435e+06	1.60283e+06	5.02588e+06
CUFF.9.1	-	-	CUFF.9	-	-	chr1:203688-204070	382	41.6301	OK	5.36082e+07	4.02061e+07	6.70102e+07
CUFF.11.1	-	-	CUFF.11	-	-	chr1:239126-239664	538	19.5995	OK	2.0562e+07	1.45634e+07	2.65605e+07
CUFF.12.1	-	-	CUFF.12	-	-	chr1:243903-244327	424	10.3509	OK	1.07542e+07	5.37709e+06	1.61313e+07
CUFF.15.1	-	-	CUFF.15	-	-	chr1:240487-240995	508	15.8596	OK	1.83065e+07	1.23671e+07	2.42459e+07


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