[ensembl-dev] "random" chromosomes form UCSC

[Sergei Manakov]

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



On 31 January 2012 01:20, Javier Herrero <jherrero at ebi.ac.uk> wrote:
> Hi Sergei
>
> These random chromosomes are not part of the official golden path. You can
> translate them into contigs using the
> http://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/chr5_random_gold.txt.gz
> file. You'll find those contigs in the Ensembl database and you can create
> slices for them.
>
> I hope this helps
>
> Javier
>
>
> On 31/01/12 08:56, Sergei Manakov wrote:
>>
>> Hello,
>>
>> In fasta files per mm9 chromosome in UCSC browser
>> (http://hgdownload.cse.ucsc.edu/goldenPath/mm9/chromosomes/) there are
>> "random" chromosome fasta files (e.g. chr5_random.fa.gz), that contain
>> some interesting sequences.
>>
>> Is it possible to retrieve a slice from ensembl for these "random"
>> chromosomes? Simply putting "5_random"
>>
>> $slice_adaptor->fetch_by_region('chromosome', "5_random", $start, $end);
>>
>> doesn't work...
>>
>> thanks!
>> Sergei
>>
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>
> --
> Javier Herrero, PhD
> Ensembl Coordinator and Ensembl Compara Project Leader
> European Bioinformatics Institute (EMBL-EBI)
> Wellcome Trust Genome Campus, Hinxton
> Cambridge - CB10 1SD - UK
>
>
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