Hi Karthik, When a particular region is viewed in the browser, we only load alignments that are in that region. We use the samtools library to do this. Also, we require an index file (.bai) in addition to the .bam file. The index file is where we get the offsets into the .bam file, given a position range. The index file is generated by samtools index. Step-by-step instructions are here: http://genome.ucsc.edu/goldenPath/help/bam.html
I hope that this information is useful. If you have further questions, please contact the mailing list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Karthik Srinivasan <[email protected]> Date: Thu, Sep 8, 2011 at 11:52 AM Subject: [Genome] Question about how custom tracks of BAM/SAM files are handled by the browser... To: [email protected] Hi, I have a question about how BAM and SAM files are handled by the genome browser? Does the software use samtools or similar APIs to work with these files? Also I have a question on how SAM/BAM files are loaded into memory: i.e. If a user wishes to view a particular region of the genome, does the browser load the entire SAM/BAM file to memory and render a track of the specific region asked for? Thanks and Regards, Karthik -- HYPERLINK "http://www.oracle.com/"; \nOracle Karthik Srinivasan | Senior Application Engineer Oracle Health Sciences Global Business Unit ORACLE India | 6'th Floor, Silver Metropolis, W.E.Highway, Goregaon(E) | 400063 Mumbai HYPERLINK "http://www.oracle.com/commitment"; \nGreen Oracle Oracle is committed to developing practices and products that help protect the environment _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
