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
