trouble visualizing data

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trouble visualizing data

Jen Hillman-Jackson
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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Jennifer Hillman-Jackson
http://galaxyproject.org
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