Hello, David, It looks as if you have not created a .bai file to go along with the .bam file. The two files must reside together in the same directory.
Please note the process for creating the .bai file using samtools, as indicated here: http://genome.ucsc.edu/goldenPath/help/bam.html Also, please check that both files are world-readable. I hope this helps. best regards, --b0b kuhn ucsc genome bioinformatics group On 4/12/2012 3:29 PM, Herndon, David wrote: > Hello UCSC Genome Browser Staff - > > We are experiencing difficulties with a custom track line for a .bam and > indexed .bam file constructed from the training set described in the recent > TopHat publication (RNA-seq with Drosophila). > > We have the sorted and indexed files available at: > > http://usda02.vetmed.wsu.edu/public_bam/ > > However when we type the following into the custom track page: > track type=bam name="My Bam" > bigDataUrl=http://usda02.vetmed.wsu.edu/public_bam/accepted_hits.sorted.bam > > we get the following error: > > Can't access My Bam's bigDataUrl > http://usda02.vetmed.wsu.edu/public_bam/accepted_hits.sorted.bam and/or the > associated index file > http://usda02.vetmed.wsu.edu/public_bam/accepted_hits.sorted.bam.bai: Error > in TCP non-blocking connect() 111 - Connection refused bamFileExists: failed > to read index corresponding to > http://usda02.vetmed.wsu.edu/public_bam/accepted_hits.sorted.bam > Is there something obvious that we're missing? > > Do we need to open a port (different than port 80)? > > Regards, > David Herndon > Molecular Biologist > USDA-ARS > Pullman, WA 99164-6630 > 509-335-6004 > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
