[ensembl-dev] "random" chromosomes form UCSC

Sergei Manakov manakov at ebi.ac.uk
Tue Jan 31 08:56:25 GMT 2012


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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