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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