[ensembl-dev] assembly mapping procedure

[Andy Yates]

Hi Hiram

I don’t believe this is on our website. Specifically the data in the chain files for the mapping you’re highlighting are from the assembly tables in the core schema. The best description of this is in:

https://github.com/Ensembl/ensembl/blob/release/110/misc-scripts/assembly/README

The quick description is to look for indexical clone usage and then backfill the remaining bits using blastz. The 37 to 38 mapping were performed using this method if I remember correctly. 

Andy

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Andrew Yates - Genomics Technology Infrastructure Team Leader, Joint-PI Ensembl Project
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> On 27 Sep 2023, at 23:45, Hiram Clawson <hiram at soe.ucsc.edu> wrote:
> 
> Good Afternoon Ensembl:
> 
> Can you supply a pointer to the documentation that describes the procedures
> used to make the 'assembly mapping' chain file available at:
> 
>  http://ftp.ensembl.org/pub/assembly_mapping/homo_sapiens/GRCh37_to_GRCh38.chain.gz
> 
> It must be close to this page somewhere:
> 
>   http://useast.ensembl.org/info/genome/compara/analyses.html
> 
> I'm looking for more detail than just 'lastz output is chained'
> 
> I know it must be somewhere on the Ensembl web site, but I'm not immediately
> finding that.  Thank you for your assistance.
> 
> --Hiram
> 
> 
> 
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