[Genome] liftOver using over.chain

[Tay Sen Kwan]

Hello,

I understand from past e-mail queries that the difference between the 
all.chain and the over.chain liftover files were that the latter contain 
"filtered results and that there are no duplicates."  I am using the 
hg18To....over.chain files to perform liftover of individual exons of 
single-copy, human cDNAs to other genomes, I would like to find out if 
there were certain families of repeats that were not filtered out in 
these files; or alternatively, what are the families of repeats that are 
filtered out ?  Many thanks.

Regards,

Sen Kwan