[ensembl-dev] "random" chromosomes form UCSC

[Hiram Clawson]

Good Afternoon Sergei:

This is correct.  Only two contigs in this chr5_random.
The coordinates are 0-based.  Almost all tables at UCSC are 0-based.
It may be more convenient for you to fetch this
information from the public MySQL server:

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e "select * from chr5_random_gold;" mm9

And the table description:

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e "desc chr5_random_gold;" mm9

Which is on the download server as:

http://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/chr5_random_gold.sql

--Hiram

Sergei Manakov wrote:
> Thanks Javier,
> 
>> translate them into contigs using the
>> http://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/chr5_random_gold.txt.gz
> 
> I opened the file and this is it's entire content:
> 
> 73  chr5_random 0   147415  1   F   AC133095.3  0   147415  +
> 73  chr5_random 197415  357350  3   F   AC147261.5  0   159935  +
> 
> It appears that not all of the chr5_random.fa is in Ensembl (for
> example, the bit  147415 to 197415) is missing. So is it true that
> parts of chr5_random.fa are not actually a part of any contig in
> golden path?
> 
> Finally, sorry if I overlooked something, but where can I find
> description of what's in *_random_gold.txt.gz files? These appear to
> be 0-based coordinates, so do I need to add 1 to them, in order to
> query ensembl via perl API?
> 
> thanks,
> Sergei