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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