[ensembl-dev] Question about missing regions in whole genome alignments

[Jason Rozick]

I had to use data from E75 and ucsc.edu.  I'm seeing assembly coverage from 2 vectors AC005666.1 and AC011195.14.  For fuller span, can look at ENST00000389934, ENST00000582740, ENST00000349033, and ENST00000240361. 


     On Wednesday, November 11, 2015 5:10 AM, Matthieu Muffato <muffato at ebi.ac.uk> wrote:
   

 Dear Marc,

Thank you for bringing this to our attention. I have looked in some of 
the debug output of the pipeline and I can see that Enredo thinks this 
human region is only found syntenic to cat in the 17-way EPO, so the 
error goes quite early in the pipeline. I still need to check whether 
the anchors were loaded correctly, but the overall coverage stats look 
fine. Unfortunately, we don't have all the files for the 8-way EPO. I'll 
let you know if I find out what happened to this region

Matthieu, Ensembl Compara

On 04/11/15 12:47, Marc P. Hoeppner wrote:
> Dear EnsEMBL developers,
>
> I've noticed that there could be a problem with certain whole genome
> alignments in the current (E82) version of EnsEMBL.
>
> Specifically, for the human region 17:58663933-58739040 (and possibly
> others).
>
> This region is syntenic on all primate genomes (8 primates EPO) as well
> as 23 amniotes (amniotes Pecan). However, in 17 mammals (EPO), this
> region is only identified as syntenic between human and cat - which I
> suspect is a mistake. I understand that Pecan and EPO use different
> algorithms, but the gene in this region (TEX14) is conserved across all
> mammals (and most vertebrates) and has no obvious homologs that may
> explain off-target alignments.
>
> Regards,
>
> Marc
>

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