Copy Number Variation Detcetion In Glaxay

6.3 years ago by

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello, The tool "FreeBayes" may be of interest. Please see the tool form for links to the primary tool documentation to see if the functionality will meet your needs. Best, Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org

ADD COMMENT • link written 6.3 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks Jen, I am also intrested in this. Has any one used FreeBayes in Galaxy or out side Gaaxy to detect CNV from a ilumina sequencing data. Is their a tutorial for running this tools. Thanks. To: shamsher jagat <kanwarjag@gmail.com> Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] copy number variation detcetion in Glaxay Hello, The tool "FreeBayes" may be of interest. Please see the tool form for links to the primary tool documentation to see if the functionality will meet your needs. Best, Jen Galaxy team -- Jennifer Jackson 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: http://lists.bx.psu.edu/

ADD REPLY • link written 6.3 years ago by Mathew Bunj • 100

Hi Mathew, To clarify, freebayes is not designed to detect CNVs. It can CNV information detected in another method to correctly genotype at sites with copy number variations. If you have exome data, there is conifer http://<http: conifer.sourceforge.net=""/> conifer.sourceforge.net/ <http: conifer.sourceforge.net=""/>. For more general applications, there is ERDS, http://www.duke.edu/~mz34/erds.htm I don't know if either of these will suit your needs. I use the CNV input methods in freebayes regularly for known, large variations in copy number, such as are seen on mammalian sex chromosomes. Best, Erik

ADD REPLY • link written 6.3 years ago by Erik Garrison • 20

Thanks Erik, I was also not very clear about Freebayes use in CNV detection. Thanks for clarifiaction. Mathew To: Mathew Bunj <mathewbunj@yahoo.com> Cc: shamsher jagat <kanwarjag@gmail.com>; Jennifer Jackson <jen@bx.psu.edu>; "galaxy-user@lists.bx.psu.edu" <galaxy- user@lists.bx.psu.edu=""> Subject: Re: [galaxy-user] copy number variation detcetion in Glaxay Hi Mathew, To clarify, freebayes is not designed to detect CNVs. It can CNV information detected in another method to correctly genotype at sites with copy number variations. If you have exome data, there is conifer http://conifer.sourceforge.net/conifer.sourceforge.net/. For more general applications, there is ERDS, http://www.duke.edu/~mz34/erds.htm I don't know if either of these will suit your needs. I use the CNV input methods in freebayes regularly for known, large variations in copy number, such as are seen on mammalian sex chromosomes. Best, Erik Thanks Jen,

ADD REPLY • link written 6.3 years ago by Mathew Bunj • 100

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