Just a quick note about a new type of custom track supported on the UCSC Genome Browser. We get a lot of questions about support for the next-gen sequencing types of data peeople are generating or expect to be generating soon. This came across the announcement mailing list yesterday. It also includes some helpful links for more details about this track and about other large data set track types.
We are pleased to announce the availability of another new track type for Custom Tracks: the Binary Alignment/Map (BAM).
BAM is the compressed binary version of the Sequence Alignment/Map (SAM) format, a compact and index-able representation of nucleotide sequence alignments. Many next-generation sequencing and analysis tools work with SAM/BAM. For custom track display, the main advantage of indexed BAM over PSL and other human-readable alignment formats is that only the portions of the files needed to display a particular region are transferred to UCSC. This makes it possible
to display alignments from files that are so large that the connection to UCSC would time out when attempting to upload the whole file to UCSC. Both the BAM file and its associated index file remain on your web-accessible server (http or ftp), not on the UCSC server. UCSC temporarily caches the accessed portions of the files to speed up interactive display.
Read more about the BAM file type here: http://genome.ucsc.edu/goldenPath/help/bam.html
Read more about the SAM project here: http://samtools.sourceforge.net/
For help with samtools, please contact the SAM tools mailing list:
Read more about other file types available for use in the genome browser for very large data sets: