[Genome] chr"N"_random

[Rachel Harte]

Hello Nathan,

The chrN_random chromosomes are a concatenation of clones with gaps of
50000 Ns between the clones as can be seen in the Assembly track on the
UCSC Genome Browser. Ensembl displays the unordered contigs as individual
contigs. So to find the position of these contigs on the chrN_random
chromosomes, you will need to look at the ctgPos table (Map Contigs
track).

In order to get the ctgPos table, you can either go to our downloads
server:

http://hgdownload.cse.ucsc.edu/downloads.html

Click on the link to human and scroll to the May 2004 (hg17) section, and
click on the "Annotation database" link to get the database downloads.
Alternatively, you can obtain the ctgPos table through the Table Browser.
You can reach this by clicking on the "Tables" link on the top blue menu
bar. The Map Contigs track is in the "Mapping and Sequencing Tracks"
group.

I hope that this helps you. Please let us know if you have further
questions.

Rachel

Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


On Thu, 12 Apr 2007, Nathan Johnson wrote:

> Hi
>
> I'm interested in mapping UCSC random chromosomes to the ensembl
> system.  Specifically HG17 random chromosomes, I believe these are a
> concatenation of sequences which are unplaced in the final assembly
> (for whichever reason), padded with 50kb of Ns.
>
> I must admit I've not used the UCSC browser an awful lot, so I do
> apologise if I'm asking a novice question.  Is there easy way I can
> aquire an assembly path for the random chromosomes? e.g. a list of
> contig ids and start and end values.
>
> Thanks
>
> Nathan Johnson
> Scientific Programmer
> European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> Email: njohnson at ebi.ac.uk
>
>
>
>
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