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.Matthews@bristol.ac.uk
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.Matthews@bristol.ac.uk mailto:D.A.Matthews@bristol.ac.uk
The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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.Matthews@bristol.ac.uk mailto:D.A.Matthews@bristol.ac.uk
The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org
Listed on the hg19 gateway page at the UCSC genome browser.
----- Original Message ----- From: "David Matthews" d.a.matthews@bristol.ac.uk To: "Jennifer Jackson" jen@bx.psu.edu Cc: galaxy-user@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,
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.Matthews@bristol.ac.uk mailto:D.A.Matthews@bristol.ac.uk
The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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:
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.Matthews@bristol.ac.ukmailto:D.A.Matthews@bristol.ac.uk
The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org
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.Matthews@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:
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.Matthews@bristol.ac.ukmailto:D.A.Matthews@bristol.ac.uk
The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org
galaxy-user@lists.galaxyproject.org
-
David Matthews -
David Matthews
-
Hiram Clawson -
Jennifer Jackson