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Old 12-20-2011, 09:29 AM   #1
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Location: Canada

Join Date: Nov 2010
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Default Upload .bam file to Galaxy, display on UCSC

The .bigwig files I make and upload to Galaxy get a "Display on UCSC browser" link. Another person in my lab made .bam files from Tophat using Galaxy and also has the Display on UCSC link. When I make .bam files on my own computer and upload them to Galaxy there's no Display on UCSC link. How can I display .bam files that I make myself (from Tophat) and upload to Galaxy on the UCSC browser? I tried uploading a .bai file as well but that didn't help.
biznatch is offline   Reply With Quote
Old 12-20-2011, 02:59 PM   #2
Location: LA

Join Date: May 2008
Posts: 78

may be transfer .bam to .bed
(tool available in Galaxy)
and then display .bed?
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Old 12-20-2011, 03:37 PM   #3
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Location: Canada

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The .bam files are up to 10 GB so a bed file would be huge, so would take a long time to upload and only small portions could be displayed at a time (500MB upload limit to UCSC). I could ultimately make a .bigbed file which I assume could be displayed from Galaxy to UCSC as I had no problems with .bigwig files but the idea is to have a relatively quick way to visualize the Tophat output in the UCSC browser.
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Old 12-20-2011, 04:12 PM   #4
Location: Oregon

Join Date: Jan 2011
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My guess is that Galaxy is not recognizing it as a BAM file (in which case change the datatype), or it is not sorted, in which case try sorting it. I think. :-)

Could also post to galaxy-user list. Subscribe here:
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