[ensembl-dev] Chimp alignment for Chromosome Y

[Kathryn Beal]

Hi Yuan,
I can confirm that these 2 regions look correct in the new release (e66):
Region 1

homo_sapiens/1-1621    TATCTCCATGGGGTCATTTTTTTTCTTTTCTTTCTTTCTCTTTTTCTTTCTTTCTTCTATTTTTTTTTTTTTTTTTTTTTTGAGACAGGATCTTGCTCTG
pan_troglodytes/1-1621 TATCTCCATGGGGTCATTTTTTTTCTTTTCTTTCTTTTTCTTTTTCTTTCTTTCTTCTATTTTTTTTTTTTTTTTTTT---GAGACAGGATCTTGCTCTG
                       ************************************* ****************************************   *******************

homo_sapiens/1-1621    TCACCCAGGCTGGAGGGCAGTGGGATGATCACTGCTCACTGCAACCCTTCACTTCTCCAAGGCTTAGGTGATCCTCCCATGATGAGGTCAATTTTTAAAG
pan_troglodytes/1-1621 TCACCCAGGCTGGAGGGCAGTGGGATGATCACTGCTCACTGAAACC-TTCACTTCTCCAAGGCTTAGGTGATCCTCCCATGATGAGGTCAATTTTTAAAG
                       ***************************************** **** *****************************************************

Region 2
homo_sapiens/1-21      TCAAGGGATCCCCAGGCTCAG
pan_troglodytes/1-21   TCAAGGGATCCCCAGGCTCAG
                       *********************

Thank you for bringing this to our attention.
Cheers
Kathryn

> 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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> 
> 
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