Hello, The simplest methods is to use the Table browser: http://genome.ucsc.edu/cgi-bin/hgTables Under the track group Mapping and Sequencing is a track called Map Contigs. The default table is ctgPos. This file has contigs labeled in NT_* format. Use the region filter to obtain data for random contigs such as region=chr1_random. These are composite "chromosomes" and all contigs are in the (+) orientation (may differ from NCBI). Name and download files, once for each random chrom.
This track can also be viewed in the Genome Browser using the track "Map Contigs". The track details page has source, methods, and credit info. And similar content is in the Downloads area, but the contigs are labeled by genbank accession. If this interests you, ftp the data from this path: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/ file is contigAgp.zip. Ftp instructions are in the README file. Thanks and please write back if you have questions or need more help, Jennifer Jackson UCSC Genome Bioinformatics Group Jimmy Lin wrote: > Hi: > > I know from the website (http://genome.ucsc.edu/FAQ/FAQdownloads#download10) > that random fasta files associated with chromosomes are data data related to > sequence that is known to be in a particular chromosome, but could not be > reliably ordered within the current sequence and now also for sequences that > is not in a finished state, but whose location in the chromosome is known, in > addition to the unordered sequence. > > However, I am interested in determining contig info for sequence matches to > the random files associated with chromosomes. Specifically, is there a table > matching e.g. chr1_random to different NCBI identifiers (e.g. NT_004434.18)? > Would chr1_random be ONE contig or conglomerate of all unmatching contigs > associated with chr1? > > thanks for you assistance. > > Jimmy > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
