[Genome] (no subject)

[Shan Yang]

Hi,

I have a question about 
<http://hgdownload.cse.ucsc.edu/goldenPath/galGal2/database/chr1_chainSelf.txt.gz>chrXX_chainSelf.txt.gz 
file (specially, I am using this data for chicken galGal2). My 
understanding is that these files record alignments of each region to 
the whole genome (chicken genome here)   and then the alignment go 
through some post-alignment processing. Is this right?
My question is: Do you mask out all repeats reported by repeatmasker 
while doing the alignment? Given the nature of repeats, I think you 
already did this but I do see chainself tracks sitting at the same 
position of a repeat. But meanwhile, if you did not mask out repeats, 
I expect to be much more chainself counts at repeats loci. I am a 
little confused...

Thank you very much!


Shan Yang, PhD
Genome Biology Division, L-441
Biosciences Directorate
Lawrence Livermore National Laboratory
7000 East Ave, Livermore, CA, 94550

Ph:  925-423-8594
Fax: 925-422-2099