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.cuffli...@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 > > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
