[galaxy-user] Cuffdiff question about using an unspecified (?) database/build
Hello! I have an RNA-Seq project which consists of 5 samples from the species tree shrew. When uploading these fastq files into Galaxy, I chose unspecified (?) for the database/build since the latest tree shrew version is not in the drop down list. When using TopHat, Cufflinks/Compare I have selected a reference genome from my history instead of using a built-in index, as well as a gtf annotation file for Cufflinks/Compare and everything has been working fine. Now, I am at the Cuffdiff step and I am running into an error when setting it up to perform replicate analysis. When I select my TopHat accepted hits bam file I see a red X and the error: Unspecified genome build, click the pencil icon in the history item to set the genome build. Here's a screenshot of what I'm seeing: [cid:image001.png@01CC5E4E.76F37AF0] Since the latest reference genome for tree shrew wasn't listed, that's why I chose unspecified (?). Should I go back and edit these accepted hits bam files to say the Database/Build from the drop down list is Tree shrew Dec. 2006 (Broad/tupBel1) (tupBel1)? I know that this is simple to change, but will this affect my results in any way? Any help/info would be greatly appreciated. Thanks, David inline: image001.png___ 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] Cuffdiff question about using an unspecified (?) database/build
Jen, Thank you very much for the reply. I'm glad to know it is a known bug and not something on my side of things. So, would my analysis be affected if I did change the bam file Database/Build to the older tree shrew version found in the drop down list? What significance does this Database/Build box have in downstream analysis if you have your own fasta reference genome file and gtf annotation file that is being referenced instead of a locally cached one? I'm just trying to obtain a better understanding of the Database/Build box for analyses where I provide the fasta and gtf file. Thanks, David -Original Message- From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: Friday, August 19, 2011 9:20 AM To: David K Crossman Cc: galaxy-user (galaxy-user@lists.bx.psu.edu) Subject: Re: [galaxy-user] Cuffdiff question about using an unspecified (?) database/build Hello David, This is a known bug. The correction is planned to be moved out onto the public Galaxy instance at the next update (within a week). Sorry for the current inconvenience, Best, Jen Galaxy team On 8/19/11 7:00 AM, David K Crossman wrote: Hello! I have an RNA-Seq project which consists of 5 samples from the species tree shrew. When uploading these fastq files into Galaxy, I chose unspecified (?) for the database/build since the latest tree shrew version is not in the drop down list. When using TopHat, Cufflinks/Compare I have selected a reference genome from my history instead of using a built-in index, as well as a gtf annotation file for Cufflinks/Compare and everything has been working fine. Now, I am at the Cuffdiff step and I am running into an error when setting it up to perform replicate analysis. When I select my TopHat accepted hits bam file I see a red X and the error: Unspecified genome build, click the pencil icon in the history item to set the genome build. Here's a screenshot of what I'm seeing: Since the latest reference genome for tree shrew wasn't listed, that's why I chose unspecified (?). Should I go back and edit these accepted hits bam files to say the Database/Build from the drop down list is Tree shrew Dec. 2006 (Broad/tupBel1) (tupBel1)? I know that this is simple to change, but will this affect my results in any way? Any help/info would be greatly appreciated. Thanks, 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support ___ 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] New built in index for Ler within galaxy
Hello Howard, To use this alternate as a reference genome: 1 - load the fasta version of the genome into your history 2 - when using tools, select the option Use reference genome from history (or similar), then select the fasta file There is no need to load the index files, only the fasta file and to make certain that Galaxy assigns the file type as fasta (using the pencil icon to access the Edit Attributes to set the datatype if necessary). Using FTP to load the data will be necessary. Instructions are on the tool form Get Data - Upload and detailed help is also available at: http://galaxyproject.org/Learn/Upload%20via%20FTP http://galaxyproject.org/Learn/Screencasts see: Tool tutorials - Using FTP Hopefully this helps! Best, Jen Galaxy team On 8/19/11 5:14 PM, Howard M. Goodman wrote: I would like to use a built in Arabidopsis Landberg erecta (Ler) index instead of TAIR10 for example for all my analysis within Galaxy. I have such an index created by Mathew McCormack and have used it successfully doing a Bowtie test run on my home computer. It has the usual 6 Bowtie index files. Can you add this to the built in indexes or is there some way to add it to my history and use it in all the programs? Thank you for you consideration. Howard The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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 http://galaxyproject.org/Support ___ 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/