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
> http://usegalaxy.org
> http://galaxyproject.org


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