Re: [galaxy-user] Displaying bed files in ucsc
Good Evening Jose: Please note the types of graphing formats you can display at UCSC: http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format I would recommend converting your bedgraph file to a bigWig file and display that via a remote URL. This would be your most efficient mechanism of display. --Hiram - Original Message - From: Xianrong Wong won...@gmail.com To: James Robinson jrobi...@broadinstitute.org Cc: galaxy-user@lists.bx.psu.edu Sent: Thursday, May 10, 2012 9:27:07 PM Subject: Re: [galaxy-user] Displaying bed files in ucsc I changed it to bedgraph and can no longer view in UCSC (the button to view in UCSC was not there anymore). I had it in bed format subsequently and put in a header. I was looking at the bedgraph/wiggle header documentation on UCSC but don't find any that describes displaying scores in histogram format. I saw that we can change colour the intensity of the bars based on scores though. Jose On Thu, May 10, 2012 at 10:27 PM, James Robinson jrobi...@broadinstitute.org wrote: Hi Jose, What you have described is a bedgraph file. Perhaps changing the file extension to bedgraph will be enough, if not you might be required to enter a track line. See UCSC for details. On Thu, May 10, 2012 at 9:04 PM, Xianrong Wong won...@gmail.com wrote: Hello, I have a bed file in this format: chr# start end scores. I tried to view it in ucsc main but it showed only where the fragments are(based on the start and end coordinates) with numerical scores beside each fragment. How do I view the file as a histogram format? What format will I need to convert the file to and where can I do the conversion? Any advise is greatly appreciated! Jose ___ 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] mount issue
Hi Zeeshan, The file system error message you saw when you first start a new cluster is, oddly enough, the expected behavior. And, like you noticed, after the cluster has been initialized for the first time, subsequent startups do not show the error. Enis On Thu, May 10, 2012 at 4:11 AM, Zeeshan Ali Shah zas...@pdc.kth.se wrote: After restart it goes away.. Zeeshan On Tue, May 8, 2012 at 4:51 PM, Zeeshan Ali Shah zas...@pdc.kth.sewrote: HI, I am getting this when start cluster first time . Error mounting file system '/mnt/galaxyData' from '/dev/sdg3', running command '/bin/mount /dev/sdg3 /mnt/galaxyData' returned code '32' and following stderr: 'mount: you must specify the filesystem type ' Is this a bug ? shd i avoid .. BR Zeeshan ___ 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/ ___ 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] Displaying bed files in ucsc
Please note the arguments you can use in a track line for a type=wiggle_0 format file: http://genome.ucsc.edu/goldenPath/help/wiggle.html The arguments useScore, scoreMin, scoreMax have no meaning with a wiggle track. A wiggle track does not display items in a gray-scale fashion, it draws a graph of the data values. --Hiram - Original Message - From: Liz Ashley lizzi...@hotmail.com To: won...@gmail.com Cc: galaxy-user@lists.bx.psu.edu Sent: Friday, May 11, 2012 6:05:14 AM Subject: Re: [galaxy-user] Displaying bed files in ucsc In the title information you need to include UseScore information including the range you want to cover with your histogram. There is a section in the UCSC website that explains the content: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 For stating the range of your histogram: scoreMin=X scoreMax=X. This will mean that the greyscale shading uses the two X values as the value for white and black, all other points will be an even range like the example on the UCSC browser page. When I was doing this the information I used was wiggle format: track type = wiggle_0 name=name of track description=description useScore=1 scoreMin=0 scoreMax=6. ChrNo StartPos FinishPos Score Hope that makes sense/helps lizzy On Thu, May 10, 2012 at 9:04 PM, Xianrong Wong won...@gmail.com wrote: Hello, I have a bed file in this format: chr# start end scores. I tried to view it in ucsc main but it showed only where the fragments are(based on the start and end coordinates) with numerical scores beside each fragment. How do I view the file as a histogram format? What format will I need to convert the file to and where can I do the conversion? Any advise is greatly appreciated! Jose ___ 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/ ___ 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/ ___ 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/ ___ 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] May 11, 2012 Galaxy Development News Brief
Dear Galaxy Community, The May 11, 2012 Galaxy Distribution has been released at: http://bitbucket.org/galaxy/galaxy-dist/ Complete News Brief http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_05_11 *Highlights:* * *EMBOSS* tools and datatypes have now moved from the _/Galaxy distribution/_ http://bitbucket.org/galaxy/galaxy-dist/ to the /Galaxy Main Tool Shed/ http://toolshed.g2.bx.psu.edu. * Tool Integration Tests http://wiki.g2.bx.psu.edu/Tool%20Shed#Using_Galaxy.27s_functional_test_framework_to_test_tools_installed_into_your_local_Galaxy_instance, Custom Tool Panel Configuration http://wiki.g2.bx.psu.edu/Tool%20Shed#Managing_the_layout_of_your_Galaxy_tool_panel, and Configurable Tool Output Locations http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files. * Improved Multiprocess Job Handling http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scaling and Enhanced OpenID http://openid.net Support. * GATK http://www.broadinstitute.org/gsa/wiki version 1.4, FreeBayes http://github.com/ekg/freebayes, Updated *Megablast* using NCBI BLAST+ http://blast.ncbi.nlm.nih.gov/Blast.cgi, Trinity http://trinityrnaseq.sourceforge.net, WormBase 2 http://www.wormbase.org, and IGB http://bioviz.org/igb/index.html external display. * Trackster http://wiki.g2.bx.psu.edu/Learn/Visualization upgrades include /strand coloring/, /interval datatype support/, and /tabix indexing/ (fast!!). * Updated *User Interface*, *Workflow-API* upgrades, and *Custom UCSC Display*. *http://getgalaxy.org* *new*: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist *upgrade*: % hg pull -u -r 17d57db9a7c0 /Thanks for using Galaxy!/ Jennifer Jackson Galaxy Team http://wiki.g2.bx.psu.edu/Galaxy%20Team 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/
[galaxy-user] FASTq sanger to Illumina FASTq
I want to convert Sanger FASTq to Illumina FASTq with a understanding that Sanger is the current option with CASAVA. Is it possible to do such conversion in Galaxy? Thanks ___ 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/
