Question: NGS ASsembly problem
gravatar for gonzalo.greif
2.5 years ago by
gonzalo.greif0 wrote:

Hi, I can't view NGS: Assembly on the left panel on galaxy, why? enter image description here

assembly • 539 views
ADD COMMENTlink modified 2.5 years ago by Jennifer Hillman Jackson25k • written 2.5 years ago by gonzalo.greif0
gravatar for Jennifer Hillman Jackson
2.5 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Those prior tools are no longer available at (the Trinity suite). Perhaps the tools in NGS: Du Novo will meet your needs. Or if the goal is to create RNA-seq assembled transcripts for expression analysis (note: this is not true assembly in the sense of creating in fasta contigs), tools in the group NGS: RNA Analysis might be what you are looking for (Cufflinks, Sailfish). If not, the Tool Shed has other assembly tool options for use in a local or cloud Galaxy - review the category "Assembly". Should your ideal target tool not be yet wrapped for Galaxy, it could be, if you have resource to do that.


The link-outs from the wiki above include many more details for Admin functions, including how to set up a local instance to install tools (and the tools used to create built-in data indexes, e.g. Data Managers) from the Tool Shed. The ability to install tools configured by default on a Cloudman instance plus includes a basic set of the most popular genomes already indexed for many tools.

And just in case it is of interest, the 101 help and tutorials linked from the top of this page can aid in learning Galaxy from a scientific perspective.

Take care, Jen, Galaxy team

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by Jennifer Hillman Jackson25k
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