Question: What Do Chromosome Codes Such As 'Chr_Random' Represent?
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gravatar for zhuwei.cug
7.0 years ago by
zhuwei.cug20
zhuwei.cug20 wrote:

Hi, all

what are the chromosome codes in plink format for , e.g. chr1_random, chr2_random? i read the document and only got the codes for chr1,chr2. but what to do with chr_random and chrUN?

thanks.

plink chromosome • 2.2k views
ADD COMMENTlink modified 7.0 years ago by Madelaine Gogol5.1k • written 7.0 years ago by zhuwei.cug20
1
gravatar for Madelaine Gogol
7.0 years ago by
Madelaine Gogol5.1k
Kansas City
Madelaine Gogol5.1k wrote:

From http://genome.ucsc.edu/FAQ/FAQdownloads#download10

Question: "What are the chrNrandom[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 chr6random. 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. chr6hla_hap1).

ADD COMMENTlink written 7.0 years ago by Madelaine Gogol5.1k
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gravatar for Matt Shirley
7.0 years ago by
Matt Shirley9.1k
Cambridge, MA
Matt Shirley9.1k wrote:

In my experience working with PLINK, the SNP data are annotated with rsid, and not chromosome/position. In that case, I cannot imagine that these contigs will have rsids associated with variant positions. What is the documentation you are referring to?

ADD COMMENTlink written 7.0 years ago by Matt Shirley9.1k
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gravatar for Wen.Huang
7.0 years ago by
Wen.Huang1.2k
Wen.Huang1.2k wrote:

PLINK would not work with those chromosome numbers (only 1-22, X, Y, XY, and M work) .For these unconventional names you might be able to assign ID to them (e.g. chr_pos) and then put them on chromosome "0" (unmapped).

ADD COMMENTlink modified 7.0 years ago • written 7.0 years ago by Wen.Huang1.2k
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