Hi Pengfei,
The "User -> Custom Builds:" form is used to set up genomes for use with
Trackster. To use custom reference genomes with tools from the left tool
panel, only the fasta dataset in the history is needed. It sounds like
you already have loaded this, but if not, do this before following the
steps below, using FTP to load if the genome is large:
http://wiki.g2.bx.psu.edu/FTPUpload
These are the steps to extract sequences with a custom genome:
1 - starting with the tool "Fetch Sequences -> Extract Genomic DNA"
2 - set "Fetch sequences for intervals in:" to be the BED file of
coordinates
3 - set "Source for Genomic Data:" to be "History"
4 - the form will refresh to reveal a new menu option, set "Using
reference file:" to be the dataset from your history that is the fasta
version of your reference genome
5 - set "Output data type:" to be "FASTA"
It is important that the chromosome/scaffold names in the BED file are
identical to the identifiers in the FASTA reference genome dataset. If
there are mismatches, an error will result and corrections to the IDs
should be made.
Hopefully this helps, but if you continue to have problems, please send
in a bug report (using the green bug icon) from the red failed Extract
job and we can provide feedback.
Best,
Jen
Galaxy team
On 2/17/12 8:25 AM, Pengfei Yu wrote:
Hi Jeremy,
Thanks for the help! I can upload fasta data for custom builds
(name:'NCI-H209-hg18'; key:'NCI-H209-V1') now. but when I try to use a
bed file specific for this custom builds to fetch sequences from this
custom genome, it gives error information that no sequences are
available for 'NCI-H209-v1'.
I might do something wrong, do you know what would be the reason?
Thanks!
Pengfei
On Fri, Feb 17, 2012 at 7:40 AM, Jeremy Goecks <jeremy.goe...@emory.edu
<mailto:jeremy.goe...@emory.edu>> wrote:
Hi Pengfei and Noa,
I suspect this was a temporary problem related to software issues
that we encountered yesterday. Please try again and let us know if
you're still having problems.
Also, note that either a FASTA dataset or a Len file is needed, but
not both. Using a FASTA dataset enables viewing genome data in
Trackster.
Best,
J.
On Feb 17, 2012, at 12:00 AM, Noa Sher wrote:
I also had exactly the same problem yesterday - glad to see that
maybe it wasn't just me.
Happy for help!
Noa
On 16/02/2012 22:24, Pengfei Yu wrote:
Dear sir or madam,
I am using galaxy public server and I am trying to build a custom
genome using the function "custom Builds" in "user" section.
I specified the Name, Key and uploaded the genome fasta file also
the chromosome length file. But when I click "submit", galaxy
gave an error information like that:
""
*Server Error:*
An error occurred. See the error logs for more information. (Turn
debug on to display exception reports here)
""
I don't know where to find the error logs and how to turn debug
on. Could you tell me how to fix the problem and upload the
custom builds?
Thanks a lot!
Pengfei
--
Pengfei Yu
Center of Biophysics and Computational Biology
University of Illinois Urbana-Champaign
Illinois, 61820, US
Cell phone:217-898-6301 <tel:217-898-6301>
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list by
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___________________________________________________________
The Galaxy User list should be used for the discussion of
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--
Pengfei Yu
Center of Biophysics and Computational Biology
University of Illinois Urbana-Champaign
Illinois, 61820, US
Cell phone: 217-898-6301
___________________________________________________________
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/
--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
___________________________________________________________
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
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use the Galaxy Development list:
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