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
F
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 pseudoaut
Listed on the hg19 gateway page at the UCSC genome browser.
- Original Message -
From: "David Matthews"
To: "Jennifer Jackson"
Cc: galaxy-u...@bx.psu.edu
Sent: Monday, March 28, 2011 2:04:02 PM
Subject: Re: [galaxy-user] Pseudo Autosomal regions in Chrs X and Y
Hi
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 y
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
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 (w
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