Good Morning Na: Please note the type of gaps between the random contigs "non-bridged" as seen in this browser view of chr1_random:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Hiram&hgS_otherUserSessionName=mm9.nonBridged.gaps Note the annotation on the gaps called 'contig no' The separate contigs are merely placed together into this artificial "chromosome" for convenience. The non-bridged gaps indicate they have no relationship to each other. These gaps are 50,000 bases of 'N'. --Hiram na liu wrote: > Hi, > I read your explanations about chrN_random files in UCSC, as shown at the > bottom of my email. > > I feel that each chrN_random file is composed of a couple of contigs. Is my > understanding correct? > > If I am correct, then my question is how you organize the contigs in single > chrN_random file?? > > Is there any "bridge"(such as NNNNN) between any two contigs? i.e. > contigA( n letter "N" are put between these two contigs)contigB??? > > Or all contigs in a single chrN_random file are connected directly? i.e. > contigAcontigB....??? > > > ****************************************************************************************************************************************** > By the way, chrUn is also created in a similar way to chrN_random file? > > > Look forward to your reply and support!!!!!!! > > Thanks > Na > ======================================================================================= > * chrN_random tables* <http://genome.ucsc.edu/FAQ/FAQdownloads#TOP> > > *Question: * > "What are the chr*N*_random_[table] files in the human assembly? Why are > they called random? Is there something biologically random about the > sequence in these tables or are they just not placed within their given > chromosomes?" > > *Response:* > In the past, these tables contained data related to sequence that is known > to be in a particular chromosome, but could not be reliably ordered within > the current sequence. > > Starting with the April 2003 human assembly, these tables also include data > for sequence that is not in a finished state, but whose location in the > chromosome is known, in addition to the unordered sequence. Because this > sequence is not quite finished, it could not be included in the main > "finished" ordered and oriented section of the chromosome. > > Also, in a very few cases in the April 2003 assembly, the random files > contain data related to sequence for alternative haplotypes. This is present > primarily in chr6, where we have included two alternative versions of the > MHC region in chr6_random. There are a few clones in other chromosomes that > also correspond to a different haplotype. Because the primary reference > sequence can only display a single haplotype, these alternatives were > included in random files. In subsequent assemblies, these regions have been > moved into separate files (*e.g.* chr6_hla_hap1). > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
