[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 a

[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 *Highlights:* * *EMBOSS* tools and datatypes have now moved from the _/Galaxy distribution

Re: [galaxy-user] /mnt/galaxyIndices/hg19/bwa/base/hg19 not found

On Wed, May 9, 2012 at 1:09 AM, Zeeshan Ali Shah wrote: > Hi, I was following screenshot and after adding workflow > http://s3.amazonaws.com/heteroplasmy/heteroplasmy_information.html > > Upon running it is mentioning that /mnt/galaxyIndices/hg19/bwa/base/hg19 > which does not exist .. i have con

Re: [galaxy-user] Displaying bed files in ucsc

With your setting of type=wiggle_0 and using bedGraph format, you happen to have selected the most inefficient mechanism of displaying this data as explained here: http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format That's the reason why you can only see a few chromosom

Re: [galaxy-user] Displaying bed files in ucsc

Thank you for the advise. I am able to view now when I use track type=wiggle_0 but I can only do it a few chr at a time which is good enough. Just curious, what track type do I type in when I want it to be bedgraph? It seems the _0 was important for wiggle. Jose On Fri, May 11, 2012 at 9:34 A

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 grap

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 s

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