[galaxy-user] View details of Tophat alignment

2013-05-30 Thread Du, Jianguang
Hi All, After I finshed Tophat alignment for RNA-seq, I took look at the details of parameters by clicking the icon View details, and I got the information as shown below: Input Parameter Value Note for rerun RNA-Seq FASTQ file 73: Filtered Groomed data1_rep2 Use a built in reference

[galaxy-user] Information for Galaxy Event Horizon

2013-05-30 Thread Sarah Maman
Dear all, Four days of training in genomics are occurring on our local instance of Galaxy (27-30 May). This training session takes place at INRA, Toulouse Auzeville, France, as part of a collaboration between Sigenae (http://www.sigenae.org/) and GenoToul bioinformatics platform

[galaxy-user] Newbie: summary or metrics of Galaxy use adoption?

2013-05-30 Thread Ramon Felciano
Hello all - I would like to evaluate Galaxy for integration with Ingenuity's NGS analytics platform, and am trying to pull together some macro materials on how Galaxy has been used and adopted by the community at large. Are there any presentations or wiki pages that summarize basic stuff like:

Re: [galaxy-user] View details of Tophat alignment

2013-05-30 Thread Jeremy Goecks
Nothing is wrong with your job, this is a bug in our code that has been corrected. You'll start seeing the correct parameter values again when we update our server early next week. Best, J. On May 29, 2013, at 11:05 PM, Du, Jianguang wrote: Hi All, After I finshed Tophat alignment

[galaxy-user] Making Public a Data Library Gives Internal Server Error

2013-05-30 Thread Rodolfo Aramayo
Hi, As Admin, I uploaded a set of files from filesystems paths Uploading is successful but when I try to make the datasets public I get the following error: Internal Server Error Galaxy was unable to sucessfully complete your request ==By The Way...NOTE how sucessfully is misspelled!! URL:

Re: [galaxy-user] tophat to cuffdiff without cufflinks

2013-05-30 Thread Jennifer Jackson
Hello, You will need to provide a GTF or GFF3 file to Cuffdiff - this is what the tool uses as a reference base to build gene, transcript, and if provided in the annotation attributes, transcript start site and protein groupings to perform the differential analysis. More details can be found

[galaxy-user] apply for a member to access into conference. thxRe: problem with registration

2013-05-30 Thread Ay Ayy
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