Hi,
I'm trying to follow up on this post, for mapping between Ensembl's scaffold names and NCBI's assembly scaffold/chromosome names.
Like in the previous post, as an example, I'm trying to that for the Marmoset genome.
I'm a newbie to Ensembl's API, so this is as much as tried so far:
my $registry->load_registry_from_db(
-host => 'ensembldb.ensembl.org', # alternatively 'useastdb.ensembl.org'
-user => 'anonymous',
-species => 'callithrix_jacchus' );
my $slice_adaptor = $registry->get_adaptor( 'Marmoset', 'Core', 'Slice' );
my @slices = @{ $slice_adaptor->fetch_all('scaffold') };
foreach my $slice (@slices) {
my $coord_sys = $slice->coord_system()->name();
my $seq_region = $slice->seq_region_name();
my $start = $slice->start();
my $end = $slice->end();
my $strand = $slice->strand();
print "Slice: $coord_sys $seq_region $start-$end ($strand)\n"; }
Thinking that this would lead the way to finding out how to print the scaffold synonyms.
But actually, @slices
ends up being empty.
So my questions are:
- Can anyone provide an example of how to obtain the synonyms of a genome's scaffold names so that it maps between Ensembl and NCBI?
- Any idea why I'm not getting any Marmoset scaffolds?
Thanks @Emily_Ensembl. Do you mean specifically for the Marmoset genome? This Ensembl page says that the genome assembly is at the scaffold level.