Hi galaxy-users

When trying to display a set of chip microarray data in UCSC main, ,
we encounter this error:

Error(s):
Error line 38879 of
http://main.g2.bx.psu.edu/root/display_as?id=3221463&display_app=ucsc&authz_method=display_at:
chromEnd larger than chrom chr21_random size (1679928 > 1679693)

Can anybody help for this?

Best,

Yongde

On Sat, Jun 25, 2011 at 11:13 AM, Jeremy Goecks <jeremy.goe...@emory.edu> wrote:
> 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
>
>
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