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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