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Old 03-27-2012, 04:26 AM   #1
Mshegrss
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Location: the World

Join Date: Mar 2012
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Default viewing Galaxy public server alignment output

Hi all,

Does anybody know how to format .sam, .bam or .bed data in order that Galaxy gives an internal link to view the data using the UCSC site? I did a lot of trial and error changes in file format, and the only promising development was that changing the file format to BigBed gave it the label "Binary UCSC BigBed file", but still with no link to a program or site that can view the data.

I tried uploading this BigBed file to UCSC as a custom track, but the upload link times out before getting anywhere. Is there a way to access the FTP domain (from outside of the UCSC) in order to transfer the file from my computer with FileZilla?

Alternatively, my BAM file output in the History offers a link to GeneTrack, but not to Ensambl or to the UCSC. GeneTrack doesn't open the file, but gives an error message, and all the help in Seqanswers and elsewhere are for installing GeneTrack into your private Galaxy instance, not the public server.

Is there another program/site better for the homology analysis itself? Basically, I'm interested in checking homology between two plasmids and ngs bacterial genomic dna. My tendancy is to use Bioedit, since the plasmids that I'm checking for chromosomal homology are in FASTA files, but Bioedit can't open my ngs data output from Galaxy.

I'd much appreciate any advice.

Last edited by Mshegrss; 04-17-2012 at 12:29 AM.
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Old 03-27-2012, 02:44 PM   #2
maubp
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BioEdit is dead software. You might find UGene a suitable replacement (free, open source).

As to the Galaxy+BAM issues... I'm not sure about that - have you tried their mailing list? Also, have you tried Galaxy's built in viewer Trackster instead?
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Old 03-29-2012, 06:20 AM   #3
Mshegrss
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Thank you very much! UGene let me open and manipulate .bam output from Galaxy!

Many thanks
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