[Genome] Fwd: Re: [Genome-mirror] I'm mapping and characterizing genome RNA-seq data on the UCSC genome grapher and Browser

[Michael J Yarus]

Help,

I'm still having the same problem; no matter how I delete data (for
example, from "manage custom tracks"), and no matter what I upload, what
is displayed remains the first data file I uploaded, and not the current
*.bed. This is true despite the fact that all user tracks disappear when
"deleted". How do I get Graphs and the Browser to accept new data?

Very puzzling,


-------- Original Message --------
Subject: Re: [Genome-mirror] I'm mapping and characterizing genome
RNA-seq data on the UCSC genome grapher and Browser
Date: Fri, 05 Nov 2010 08:25:40 -0700
From: Katrina Learned <kat...@soe.ucsc.edu>
To: Michael J Yarus <michae...@colorado.edu>
CC: genome...@soe.ucsc.edu

Hi Michael,

Click on "Genomes" in the top dark blue bar, click the "manage custom
tracks" button, select the check box next to the data you would like to
delete and click the "delete" button. A few other ways of deleting your
data sets are described in the "Deleting Data" section of this page:
http://genome.ucsc.edu/goldenPath/help/hgGenomeHelp.html#DataSets.

You should be able to upload more than one set of data. As the note
warns on the genome graphs "upload" page, if you are uploading more than
one data set please make sure you give them different names. Only the
most recent data set of a given name is kept. Once you have your data
sets loaded, you should be able to compare them by going to the
"configure" button and increasing the "lines of graphs:" to the number
of data sets you'd like to see at once. Click submit. Now you should be
able to select different data sets in the different graph lines and see
them displayed together.

In the future, please direct your questions to the genome mailing list
at gen...@soe.ucsc.edu. This genome-mirror list is reserved for
questions about genome browser mirrors.

Katrina Learned
UCSC Genome Bioinformatics Group


Michael J Yarus wrote, On 11/05/10 07:48:
> Things are going well and getting interesting, but I cannot get Graph to
> give up the first data I sent it. It will not accept a second *.bed for
> comparison, and will not look at new, unseen data at all. Upload goes
> well, but new data never appears in the genome graph. I have read the
> instructions, even tried deleting my ucsc cookie, but nothing helps. Do
> these symptoms suggest a solution to you?
>
> thanks & cheers,
>

[Katrina Learned]

Hi Michael,

I have a few questions that I hope will help trouble-shoot this issue:

Do you get an error when you try to upload the new file?
If not, after uploading, do you get a screen that is titled, "Data
Upload Complete" with an OK button to click?
After clicking OK, when you are in the main genome graphs page, if you
click on the drop-down menu next to "graph" do you just see the original
data set? You should see all the files you've uploaded in this list, and
you should be able to select the new data set from this list and see it
in the genome graphs.

Are you using Genome Graphs on a mirror site, or are you using
http://genome.ucsc.edu/cgi-bin/hgGenome?

Thanks,

Katrina Learned
UCSC Genome Bioinformatics Group

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