[ensembl-dev] Chimp alignment for Chromosome Y

[yuan]

Thanks Kathryn, it worked when using LASTZ_NET.

There is slightly problem when I checked for the two regions on release
65:
region 1: Y:7387430-7387460, given human-chimp alignment :

Homo sapiens >  	chromosome:GRCh37:Y:7387430:7387460:1
Pan troglodytes >  	chromosome:CHIMP2.1.4:Y:24975139:24975169:-1

Homo sapiens     TTGCTCTGTCACCCAGGCTGGAGGGCAGTGG
Pan troglodytes  CTTGCTCTGTCACCCAGGCTGGAGGGCAGTG

there is 1 base shift.

region 2 : Y:13956063-13956083

Homo sapiens >  	chromosome:GRCh37:Y:13956063:13956083:1
Pan troglodytes >  	chromosome:CHIMP2.1.4:1:222316894:222316914:1

Homo sapiens     TCAAGGGATCCCCAGGCTCAG
Pan troglodytes  GGCTCAAGGGATCCCCAGGCT

there are 3 bases shift.

Hope this can be fixed next time.

yuan

On Fri, 27 Jan 2012 13:39:07 +0000, Kathryn Beal <kbeal at ebi.ac.uk> wrote:
> 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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