The bigChain format describes a pairwise alignment that allow gaps in both sequences simultaneously, just as Chain files do, but bigChain files are compressed and indexed as bigBeds. bigChain files are created using the program bedToBigBed with a special AutoSQL file that defines the fields of the bigChain. The resulting bigChain files are in an indexed binary format. The main advantage of the bigChain files is that only portions of the files needed to display a particular region are transferred to UCSC. So for large data sets, bigChain is considerably faster than regular Chain files. The bigChain file remains on your web accessible server (http, https, or ftp), not on the UCSC server. Only the portion that is needed for the chromosomal position you are currently viewing is locally cached as a "sparse file". For complete bigChain format definitions please see the bigChain help page.
+ The bigNet format describes a net, which says which parts of one genome line up with which parts of another. A net is built from chains and sorts them into levels, so it shows which alignment is the real counterpart of a region rather than just one of many possible ones. bigNet files hold the same data as Net files, but they are compressed and indexed as bigBeds. bigNet files are created using the program bedToBigBed with a special AutoSQL file that defines the fields of the bigNet. The resulting bigNet files are in an indexed binary format. The main advantage of the bigNet files is that only portions of the files needed to display a particular region are transferred to UCSC. So for large data sets, bigNet is considerably faster than regular Net files. The bigNet file remains on your web accessible server (http, https, or ftp), not on the UCSC server. Only the portion that is needed for the chromosomal position you are currently viewing is locally cached as a "sparse file". + For complete bigNet format definitions please see the + bigNet help page.
+The bigPsl format stores alignments between two sequences, as PSL files do, but they are compressed and indexed as bigBeds. bigPsl files are created using the program bedToBigBed with a special AutoSQL file that defines the fields of the bigPsl. The resulting bigPsl files are in an indexed binary format. The main advantage of the bigPsl files is that only portions of the files needed to display a particular region are transferred to UCSC. So for large data sets, bigPsl is considerably faster than regular PSL files. The bigPsl file remains on your web accessible server (http, https, or ftp), not on the UCSC server. Only the portion that is needed for the chromosomal position you are currently viewing is locally cached as a "sparse file". For complete bigPsl format definitions please see the bigPsl help page.
The bigGenePred format stores annotation items that are a linked collection of exons, much as BED files indexed as bigBeds do, but bigGenePred has additional information about the coding frames and other gene specific information in eight additional fields. bigGenePred files are created using the program bedToBigBed with a special AutoSQL file that defines the fields of the bigGenePred. The resulting bigBed files are in an indexed binary format. The main advantage of the bigBed files is that only portions of the files needed to display a particular region are transferred to UCSC. So for large data sets, bigBed is considerably faster than regular BED files. The bigBed file remains on your web accessible server (http, https, or ftp), not on the UCSC server. Only the portion that is needed for the chromosomal position you are currently viewing is locally cached as a "sparse file". For complete bigGenePred format definitions please see the