Upload .bam file to Galaxy, display on UCSC

biznatch · 12-20-2011, 09:29 AM

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.

rebrendi · 12-20-2011, 02:59 PM

may be transfer .bam to .bed
(tool available in Galaxy)
and then display .bed?

biznatch · 12-20-2011, 03:37 PM

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.

tnabtaf · 12-20-2011, 04:12 PM

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: http://lists.bx.psu.edu/listinfo/galaxy-user

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12-20-2011, 09:29 AM	#1
biznatch Senior Member Location: Canada Join Date: Nov 2010 Posts: 124	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.

12-20-2011, 02:59 PM	#2
rebrendi ng Location: LA Join Date: May 2008 Posts: 78	may be transfer .bam to .bed (tool available in Galaxy) and then display .bed?

12-20-2011, 03:37 PM	#3
biznatch Senior Member Location: Canada Join Date: Nov 2010 Posts: 124	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.

12-20-2011, 04:12 PM	#4
tnabtaf Member Location: Oregon Join Date: Jan 2011 Posts: 53	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: http://lists.bx.psu.edu/listinfo/galaxy-user