Hi Lindsey,
I see a few potential problem areas here. Double check these things:
1. when uploading, if the files are over 2G, or close to that, use FTP
instead of a browser upload. Here is how:
https://wiki.galaxyproject.org/FTPUpload
2. do not use the option to convert spaces to tabs. I doubt this does
anything to a compressed format like BAM, but you almost never want to
use this. Really is only for hand entered or pasted in data.
3. Try to convert the file to SAM to see if that functions. This will do
two things: confirm basic BAM format is intact and permit you to examine
the sequence identifiers on the header. Or try a tool like Picard's 'BAM
Index Statistics'.
4. There could be an identifier mismatch problem between your data and
our internal reference genome. The only ways to check are to either run
some type of job that will list out our genome's sequences in the UI
(like a small mapping job that creates a Galaxy-native BAM/SAM file) or
obtain our version of the genome by rysnc and compare your files against
it locally (before uploading to Galaxy). Both have advantages. The rsync
server instructions are here, and I happened to use the genome question
from yesterday to fill in the example last night, so you have near-exact
instructions!
https://wiki.galaxyproject.org/Admin/UseGalaxyRsync
5. If all else fails, consider loading the genome that you used to do
the mapping up to Galaxy as a Custom reference genome:
https://wiki.galaxyproject.org/Support#Custom_reference_genome
https://wiki.galaxyproject.org/Support#Reference_genomes
There have been some UI delays, but these are transient. Resubmitting
the action has been working, so try that if buttons do not respond the
first time.
Let us know if you continue to have problems,
Jen
Galaxy team
On 4/11/14 9:20 AM, Lindsey Fallis wrote:
Hi Jennifer,
I’m a post doc working with Brenda Oppert (she contacted you yesterday with
some problems). I too have been having some problems getting visualizations to
work. My goal is to show the Tribolium genome as a Circster plot with my
RNA-seq data laid on top. My RNA-seq data is currently in .bam format. So far
what I have a attempted to do is upload my .bam files into Galaxy using the Get
Data, upload file from computer functions. Then I choose my file, check the
‘convert spaces to tabs’ box and set the genome to Tcas. It uploads correctly.
Then I ask it to visualize as Circster and nothing happens… Then I tried
viewing in trackster and nothing happens OR I get an error message saying one
of my sequences isn’t in the genome file. Any suggestions to get the
visualizations to work so that I have the Tcas chromosomes as the Circster
backbone and my RNA-seq data showing around it?
Thank you!
Lindsey
--
Jennifer Hillman-Jackson
http://galaxyproject.org
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