Hello, Moshe, Here are some tips about getting .bam and .bb files into Custom Tracks. You will have to contact the Galaxy helpdesk about how to make a url that that can be useful for that purpose. I do not know if Galaxy can make the files available to the web for you, or if you will have to download them to your own server.
1. For bigBed: the .bb file must be available on a public http or ftp server; then use its URL to make a track line as in http://genome.ucsc.edu/goldenPath/help/bigBed.html 2. For bam: both the .bam and the .bam.bai files must be available in the same directory on a public http or ftp server. Use the .bam URL to make a track line as in http://genome.ucsc.edu/goldenPath/help/bam.html Galaxy help is here: http://wiki.g2.bx.psu.edu/Support regards, --b0b kuhn ucsc genome bioinformatics group On 3/27/2012 5:05 AM, משה גרוס/Moshe Gross wrote: > 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 two > sets of 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 data. > > I'd much appreciate any advice. > > Moshe Gross > MSc student > Department of Molecular Biology > Integrative Brain Science Center - Ariel (IBSCA) > Ariel University Center of Samaria > Ariel 44837 > Israel > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
