Greetings,
I am having trouble graphing my data-sets. No matter what data values I use I
always get back the exact same graph. I made sure I was calling it a different
name so that it didn't overwrite the old data-set. I can email the graph to you
if you want to see it. The correlation coefficient between two completely
different data sets is 1. This indicates that my data isn't really being
graphed
at all. It seems to be using a default data set each time rather than the data
I
import. I have tried clicking "Click here to reset the browser user interface
settings to their defaults." I am still getting the same problem.
The steps I am taking to get this error are as follows:
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1) click the "manage customer tracks" in the "Genomes" page. With the following
settings:
clade genome assembly position or search term gene image width
Mammal Vertebrate Deuterostome Insect Nematode Other Chicken Zebra finch
Lizard X. tropicalis Zebrafish Tetraodon Fugu Stickleback Medaka Lamprey Dec.
2008 (Zv8/danRer6) July 2007 (Zv7/danRer5) Mar. 2006 (Zv6/danRer4) May 2005
(Zv5/danRer3)
Click here to reset the browser user interface settings to their defaults.
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2) Add custom tracks
3) Copy and paste in data from a bed file. Here is a sample of the data:
browser position chr1:44006-44066
track name="leukemia_immatureT"
#Chromosome StartPosition EndPosition RegionName Score
chr1 44006 44066 region_0 0.727264185479
chr1 46023 46083 region_1 0.560017387231
chr1 47390 47601 region_2 2.02842618698
chr1 48251 48311 region_3 0.0196590689408
chr1 80315 80375 region_4 0.0588082434926
chr1 83080 83140 region_5 0.212616217385
chr1 84485 84545 region_6 0.303664994145
4) Repeat steps 1-3 for a dataset with different name and different values.
5) Click on "Home link", then "Genome Graphs" link.
6) Change settings: <b>Your browser does not support JavaScript so some
functionality may be missing!</b> <b>Your browser does not support
JavaScript so some functionality may be missing!</b>
clade: Mammal Vertebrate Deuterostome Insect Nematode Other genome: Chicken
Zebra finch Lizard X. tropicalis Zebrafish Tetraodon Fugu Stickleback Medaka
Lamprey assembly: Dec. 2008 (Zv8/danRer6) July 2007 (Zv7/danRer5) Mar. 2006
(Zv6/danRer4) May 2005 (Zv5/danRer3)
7) Click on "import" btn
8) Change settings:
group: Custom Tracks Mapping and Sequencing Tracks Genes and Gene Prediction
Tracks mRNA and EST Tracks Expression and Regulation Comparative Genomics
Variation and Repeats All Tracks All Tables track: hlk84_input
leukemia_immatureT
table: ct_hlk84input_2741
name of data set:
description:
display min value: max value:
label values: 9) Click "submit" see message:
Table Import in Progress
<b>Your browser does not support JavaScript so some functionality may be
missing!</b>
Read in 29743 markers and values in chromosome base format.
These data are now available in the drop-down menus on the main page for
graphing.
That is Strange that it says "Read in 29743 markers" when I only included 7
regions for this example.
10) Click Ok.
11) Change settings:
graph -- nothing -- Hulk84 VS Input 1 Hulk VS Input 1 in black blue purple red
orange yellow green gray
graph -- nothing -- Hulk84 VS Input 1 Hulk VS Input 1 in
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As I look at my two different graphs they look exactly the same. The data I
just
imported does not match the data in the graph.
Thank you for your help with this problem. I am so close I can taste it!
Joseph
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Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
