Fantastic, many thanks!

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






On 29 Mar 2011, at 00:19, Jennifer Jackson wrote:

> 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>
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> ___________________________________________________________
>>>> The Galaxy User list should be used for the discussion of
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>>> 
>>> --
>>> Jennifer Jackson
>>> http://usegalaxy.org
>>> http://galaxyproject.org
>> 
>> 
> 
> -- 
> Jennifer Jackson
> http://usegalaxy.org
> http://galaxyproject.org

___________________________________________________________
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