Hi David,

The PAR regions are documented at UCSC on the hg19 genome gateway page (and for some other recent genomes). Start at the main page, click into Genomes, select hg19, then scroll down to credits:

http://genome.ucsc.edu/

quote:

The Y chromosome in this assembly contains two pseudoautosomal regions (PARs) that were taken from the corresponding regions in the X chromosome and are exact duplicates:

chrY:10001-2649520 and chrY:59034050-59363566
chrX:60001-2699520 and chrX:154931044-155260560

Hopefully this helps!
Jen

On 3/28/11 2:04 PM, David Matthews wrote:
Hi,

Again, thanks for the feedback. I made my own female hg19 by deleting chrY from 
my copy of hg19 so thats OK. It still leaves the problem of how to analyse male 
transcriptomes since maps to PAR1 and 2 genes get reported as multimap reads 
which can end up being filtered out depending on how you analyse your 
transcriptome. If I knew with certainty where PAR1 and 2 are on chrY of hg19 I 
was planning to replace the nucleotides with N's on chrY so that they would no 
longer show up as a multimap problem - do you (or anyone else) happen to know 
the co-ordinates on hg19?

Cheers
David


On 23 Mar 2011, at 14:19, Jennifer Jackson wrote:

Hi David,

Right now we don't have anything built-in to filter out this type of 
duplication automatically.

As a potential option, did you know that we offer a "Canonical Female" build 
for certain genomes? This may help with some of the duplication issues, if the loss of 
novel Y is OK for your project.

Please see:
https://bitbucket.org/galaxy/galaxy-central/wiki/GenomeData

Thanks for bringing up a good point!

Best,
Jen


On 3/10/11 8:44 AM, David Matthews wrote:
Hi All again,

A separate point about the analysis of cufflinks data is the subject of
the Pseudo Autosomal Regions in X and Y - this will make a mess of gene
expression analysis in some cases especially because tophat will assign
a read to both places which therefore makes it a multihit read (which
you might then filter out) or it may double the true levels of reported
expression. Anyone had experience/thoughts on this?

Best Wishes,
David.

__________________________________
Dr David A. Matthews

Senior Lecturer in Virology
Room E49
Department of Cellular and Molecular Medicine,
School of Medical Sciences
University Walk,
University of Bristol
Bristol.
BS8 1TD
U.K.

Tel. +44 117 3312058
Fax. +44 117 3312091

d.a.matth...@bristol.ac.uk<mailto:d.a.matth...@bristol.ac.uk>








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Jennifer Jackson
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http://galaxyproject.org
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