[ensembl-dev] Chimp alignment for Chromosome Y

[Kathryn Beal]

Hi Yuan,
The human vs chimp alignments in e65 were run using lastz instead of blastz and hence the results have a method_link type of LASTZ_NET not BLASTZ_NET. 

Cheers
Kathryn

> Hi ALL,
> 
> I am using Ensembl Compara to pull out chimp sequences for corresponding human bases, most of them are correct, but for a few of them, I got  chimp bases that are different from human reference base, but UCSC has the same base as human reference base :
> 
> Ensembl API version is 63
> genomedb_name is homo_sapiens
> genomedb_name is pan_troglodytes
> alignment_type is BLASTZ_NET
> chimp_slices is 1
> num slice is 1
> name of the slice is pan_troglodytes
> ref_base is G and ref_pos is 2691796 and chimp base is A and chimp_pos is 23773099 and 1
> chimp_slices is 1
> num slice is 1
> name of the slice is pan_troglodytes
> ref_base is G and ref_pos is 2750827 and chimp base is T and chimp_pos is 23713497 and 2
> chimp_slices is 1
> num slice is 1
> name of the slice is pan_troglodytes
> ref_base is A and ref_pos is 2836431 and chimp base is T and chimp_pos is 23626512 and 3
> chimp_slices is 1
> num slice is 1
> .............. 
> 
> 
> When I changed to run ensembl version 65, I got error message :
> 
> -------------------- WARNING ----------------------
> MSG: No Bio::EnsEMBL::Compara::MethodLinkSpeciesSet found for
> <BLASTZ_NET> and homo_sapiens(GRCh37), pan_troglodytes(CHIMP2.1.4)
> FILE: Compara/DBSQL/MethodLinkSpeciesSetAdaptor.pm LINE: 681
> CALLED BY: svn/modules/AncestralBase.pm  LINE: 122
> Ensembl API version = 65
> ---------------------------------------------------
> 
> -------------------- EXCEPTION --------------------
> MSG: [] is not a Bio::EnsEMBL::Compara::MethodLinkSpeciesSet
> STACK Bio::EnsEMBL::Compara::DBSQL::AlignSliceAdaptor::fetch_by_Slice_MethodLinkSpeciesSet /nfs/team19/yuan/ensembl-checkout/ensembl-compara-65/modules/Bio/EnsEMBL/Compara/DBSQL/AlignSliceAdaptor.pm:138
> STACK AncestralBase::get_ancestral_allele_by_slices_from_db /nfs/users/nfs_y/yuan/sanger/src/svn/modules/AncestralBase.pm:135
> STACK main::get_base_from_pos_file ./get_ancestral_allele.pl:111
> STACK toplevel ./get_ancestral_allele.pl:51
> Ensembl API version = 65
> ---------------------------------------------------
> Ensembl API version is 65
> genomedb_name is homo_sapiens
> genomedb_name is pan_troglodytes
> alignment_type is BLASTZ_NET
> 
> Any idea what went wrong please?
> 
> Thanks
> 
> yuan_______________________________________________
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