Pseudo Autosomal Regions In Chrs X And Y

Question: Pseudo Autosomal Regions In Chrs X And Y

7.7 years ago by

United Kingdom

David Matthews • 630 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

rna-seq cufflinks • 925 views

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modified 7.7 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.7 years ago by David Matthews • 630

7.7 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

ADD COMMENT • link written 7.7 years ago by Jennifer Hillman Jackson ♦ 25k

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

ADD REPLY • link written 7.7 years ago by David Matthews • 630

Listed on the hg19 gateway page at the UCSC genome browser. To: "Jennifer Jackson" <jen@bx.psu.edu> Cc: galaxy-user@bx.psu.edu 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 ___________________________________________________________ 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: http://lists.bx.psu.edu/

ADD REPLY • link written 7.7 years ago by Hiram Clawson • 260

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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

ADD REPLY • link written 7.7 years ago by Jennifer Hillman Jackson ♦ 25k

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

ADD REPLY • link written 7.7 years ago by David Matthews • 630

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