[ensembl-dev] compara blastz coordinates

[Elena Grassi]

Hello,

I've looked around in the documentation but I'm not finding a straight
answer so I'm posting here, I hope that this is not a very well hidden
faq :)

I'd like to download BlastZ-net/Lastz-net alignments from compara and
store them in axt format. I'm using the APIs version 57 and from this
source code:
ftp://ftp.ensembl.org/pub/ensembl-compara/scripts/hcr/subsetAxtFromAndToCompara.pl
and the UCSC documentations about axt:
http://genome.ucsc.edu/goldenPath/help/axt.html
I assumed that the non-reference species coordinates where given on
the reverse complement strand when alignments fall on the negative
strand but some manual tests via mysql seems to indicate that
coordinates are always absolute (on the positive strand).

Can someone help me?
Thanks,
Elena Grassi
-- 
http://www.mbcunito.it/