Hello,

The error is indicating that the end of your dataset is larger than the chromosome it is aligned to for this line (at least). This is expected when attempting display of certain data types at UCSC.


This is a known issue. You can either remove these lines from your dataset with tools in Text Manipulation, download the data & trim coordinates using unix tools you design or obtain from UCSC, or best: view in Trackster ("Visualization").

Hopefully one of these solution will work for you,

Best,

Jen
Galaxy team

ps: For next time, it would be very helpful for us if you would start over in a completely fresh/new thread email when starting another discussion topic, to help us track and answer the most effectively. Thanks!

On 6/27/11 9:48 AM, YBao wrote:
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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___________________________________________________________
The Galaxy User list should be used for the discussion of
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--
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http://usegalaxy.org/
http://galaxyproject.org/
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