Re: [Galaxy-Bugs] Workflow Database

Question: Re: [Galaxy-Bugs] Workflow Database

8.8 years ago by

Jeremy Goecks • 2.2k wrote:

Hi Jason, In the last couple weeks we've written the infrastructure that (a) enables users to publish workflows and (b) provides a way to browse, search, view, and use published workflows. (Histories and pages will have the same functionality as well.) This code is making it's way to our main webserver (it's being tested right now), and it should become available within the week. FYI, the links for published items will be: http://main.g2.bx.psu.edu/workflow/list_published http://main.g2.bx.psu.edu/history/list_published http://main.g2.bx.psu.edu/page/list_published Finally, a good place to pose these types of questions is galaxy-user, which I've CC'ed Best, J.

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modified 7.3 years ago by Peng, Tao • 170 • written 8.8 years ago by Jeremy Goecks • 2.2k

7.8 years ago by

Jeremy Goecks • 2.2k

Jeremy Goecks • 2.2k wrote:

Brandon, These type of questions--questions about to use Galaxy--are best directed to the galaxy-user list, so I've moved it there. This is correct: Galaxy now supports an arbitrary number of input files to cuffcompare, making repeated merging unnecessary. Cuffdiff claims to support biological replicates, and, as you found, Galaxy provides the infrastructure to specify replicates to Cuffdiff. I do not know the statistical methods used for analysis, but this would be a good question to ask either on seqanswers or on the new tophat-cufflinks mailing list: tophat.cufflinks@gmail.com This is because the p_id attribute is not being attached to the combined_transcripts dataset produced by Cuffcompare. This problem is due to your reference file being incorrect -- it should be dataset 81, your reference annotation. Thanks, J.

ADD COMMENT • link written 7.8 years ago by Jeremy Goecks • 2.2k

7.7 years ago by

Jeremy Goecks • 2.2k

Jeremy Goecks • 2.2k wrote:

Brandon, You can manage your subscription to galaxy-user here: http://lists.bx.psu.edu/listinfo/galaxy-user/ Correct. You can find full details of Cuffdiff's outputs in the manual: http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff_output J.

ADD COMMENT • link written 7.7 years ago by Jeremy Goecks • 2.2k

7.7 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello, Yes, and this tutorial can help to get you oriented: http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise Please let us know if we can help more (using galaxy-user@bx.psu.edu please for data/tool questions), Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

ADD COMMENT • link written 7.7 years ago by Jennifer Hillman Jackson ♦ 25k

7.3 years ago by

Peng, Tao • 170

Peng, Tao • 170 wrote:

Hi Jen, I have RNA-seq data for 2 biologial samples loaded in to galaxy. The samples are from human skin biopsies from genital herpes reactivation. Using Tophat I will align the reads to human genome. But I am NOT how to build genital herpes genome (HSV-2) and aligh reads to HSV-2 genome? Any suggestion is greatly appreciated! Thanks, tao To: Peng, Tao; galaxy-bugs@bx.psu.edu Subject: Re: [galaxy-bugs] loading data Hello, Glad to hear that you were able to load your data. When logged in, FTP loaded data will initially be in the FTP upload area under the "Get Data -> Upload" tool (in the center pane). From here, load data into the history that you wish to work with. If you are not sure where this is exactly, please note the graphics in the FTP wiki and screencast. As a reminder, please send all new and followup questions with a to or cc to the mailing list, not to individual team members. This is important for our team to be able to track and answer questions. We would appreciate your helping out with this going forward. Hopefully this helps. Jen Galaxy team see itself. which load at: the or the FTP and to different used on community and sample. -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

ADD COMMENT • link written 7.3 years ago by Peng, Tao • 170

Hellp Tao, When using a custom reference genome, the file must be in fasta format and the datatype must be set as fasta (use pencil icon to modify "Edit Attributes" as needed). Any fasta file is allowed, however those with simplified identifiers (no pipes "|", in particular) tend to have less problems with certain tools. If there are errors, the most likely cause is formatting. If there are problems and you cannot resolve the format issue, please send a bug report associated with a failed mapping run using the custom reference genome. Use the green bug icon for the failed dataset when reporting the error (instead of screenshots). I will watch for your bug report. If you use a different email than this one for your galaxy account, please note that in the bug report comments area so that I can link the two threads. Thanks, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

ADD REPLY • link written 7.3 years ago by Jennifer Hillman Jackson ♦ 25k

Hi jen, I have used BOWTIE to align my RNA-seq reads to HSV2 genome; out of 35,000,000 lines, only 621 lines left when I chose to have mapped reads only. How can visualize these aligned reads to HSV-2 genome? In the panel of converted SAM to BAM, I tried to use the data in trickster, but I am not sure to how to build a HSV genome as a reference? I appreciate your help, tao

ADD REPLY • link written 7.3 years ago by Peng, Tao • 170

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