[galaxy-user] Removal of duplicates and Cufflinks usage
Hi All I've started analyzing my RNA-Seq data for two time points: Day0 and Day4 for control and treated. I've done aligning the data to the reference genome using Tophat. I've removed duplicates from the data sets. Could somebody please tell me, how important is it to remove duplicates and how will it influence my results if I don't remove? I want to start with Cufflinks all the way through to Cuffdiff. Where do I start since there are just so many options (in the manual) to choose from? What do I look for? Kind regards Lizex Disclaimer This message is confidential and may be covered by legal professional privilege. It must not be read, copied, disclosed or used in any other manner by any person other than the addressee(s). Unauthorised use, disclosure or copying is strictly prohibited and may be unlawful. The views expressed in this email are those of the sender, unless otherwise stated. If you have received this email in error, please contact ARC Service Desk immediately. (mailto:serviced...@arc.agric.za) To report incidents of fraud and / or corruption in the ARC use our Ethics Hotline by: Phone number : 0800 21 20 56 Fax number : 0800 200 796 Email address : fr...@kpmg.co.za For more information on the ARC Ethics Hotline, please visit our website at www.arc.agric.za. ___ 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/
[galaxy-user] BWA install problem
Hi, I am trying to run Galaxy locally and downloaded BWA but I can't get it to run. Do I have to use 0.5.6 or can I use 0.5.9? The make command does not work with ver. 0.5.9. Thanks, Christopher W. Callaway University of Utah Dept. of Pediatrics Division of Neonatology 417 Wakara Way # Salt Lake City, UT 84108 ___ 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/
Re: [galaxy-user] BWA install problem
Hello Christopher, The most current version of the BWA wrapper is designed to work with version 0.5.9. This is true if you are pulling from the development repository or the distribution: http://bitbucket.org/galaxy/galaxy-central/src/21138a4a1fea/tools/sr_mapping/bwa_wrapper.py http://bitbucket.org/galaxy/galaxy-dist/src/338ead4737ba/tools/sr_mapping/bwa_wrapper.py The documentation in our wiki is slightly outdated and does note 0.5.6 - I will correct this today. http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup Perhaps you are running an older version of Galaxy? Support for the newer BWA version was incorporated on 2011-05-09: http://bitbucket.org/galaxy/galaxy-dist/history/tools/sr_mapping/bwa_wrapper.py Please let us know if we can help further. It may be best to post this sort of question to the galaxy-...@bx.psu.edu mailing list in the future, if you are interested in development community feedback (the dev list is for install/development topics). http://galaxyproject.org/wiki/Support Best, Jen Galaxy team On 11/4/11 11:08 AM, Christopher Callaway wrote: Hi, I am trying to run Galaxy locally and downloaded BWA but I can’t get it to run. Do I have to use 0.5.6 or can I use 0.5.9? The make command does not work with ver. 0.5.9. Thanks, Christopher W. Callaway University of Utah Dept. of Pediatrics Division of Neonatology 417 Wakara Way # Salt Lake City, UT 84108 ___ 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/ -- Jennifer Jackson http://usegalaxy.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/
[galaxy-user] Uploading Genome from Ensembl
How do I upload the Zebrafish genome from Ensembl to my user history in Galaxy? I'm trying to map my RNA-Seq data using TopHat and need to map it to the Ensembl version of ZFv9, but Galaxy only has the UCSC version built in. The Ensembl version is slightly different. Thanks, Sheena ___ 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/
