Galaxy Help

Question: Galaxy Help

5.8 years ago by

1. To Whom it May Concern: I am using the Galaxy interface, and according to the tutorial screencast, I should be able to upload my own reference genome. The address given in the tutorial (http://galaxyproject.org/FTPUpload) leads to a 404 file not found page. I was wondering if there is an alternative site that can allow me to do this. Also, I tried to use the est2genome tool in order to try and align my uploaded sequences. It would only allow me to compare two sequences at a time. Is it possible to align a larger number of sequences at once? I understand there are other programs that allow for this kind of procedure (e.g. Sequencher), but I would like to do this in Galaxy. Thank you for your time, -- -John G. Phillips Graduate Research Assistant University of Tulsa 231-233-6914

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modified 5.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.8 years ago by John Phillips • 10

5.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi John, The current link is: http://wiki.galaxyproject.org/FTPUpload We changed our wiki base and many of the older links do not redirect. I'll let our wiki admin Dave know about this and see what can be done. If this comes up again soon, the base always redirects to "http://galaxyproject.org -> http://wiki.galaxyproject.org", and clicking into "Learn" will likely take to you want to go - the primary hub page for user documentation - including the links in tutorials (plus the wiki side navigation bar with a few different search options). And is true that we do not offer large scale EST to genomic alignment on the public server. Galaxy choices such as BLAST+/Megablast are for use with a local or cloud Galaxy instance. When using a local instance, the tool wrapper can be obtained from the Tool Shed (http://toolshed.g2.bx.psu.edu). A cloud ami would have these tools as part of the package. You can also check the Tool Shed for other options - more are added all the time. Local: http://getgalaxy.org Cloud: http://usegalaxy.org/cloud Hopefully this helps, Jen Galaxy team -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

ADD COMMENT • link written 5.8 years ago by Jennifer Hillman Jackson ♦ 25k

5.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi John, If you have other sequence types, there are other alignment tool choices on the public Main server. The est2genome tool has a fairly specific use, so I thought that this was your input/goal. For ChIP-seq, RNA-seq, or other NGS datatypes, please see the tools under 'NGS: Mapping' and 'NGS: RNA Analysis'. We have tutorials for these tools - from the top menu bar follow 'Shared Data -> Published Pages". Good places to start are 'Galaxy Exercises', 'Galaxy RNA-seq Analysis Exercise', and 'Using Galaxy' (but review the others as wanted, I am not sure what type of data you are working with). More tutorials are in our wiki here: http://wiki.galaxyproject.org/Learn#Other_Tutorials Other public Galaxy sites offer specialized tools for working with certain data types - the best way to find out what they have to is visit them and review. We keep a list of links in our wiki here: http://wiki.galaxyproject.org/Big%20Picture/Choices -> http://wiki.galaxyproject.org/PublicGalaxyServers Good luck with your project! Next time, or if you have followup, please be sure to leave the mailing list in the cc to help us with tracking. Thanks! Jen Galaxy team -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

ADD COMMENT • link written 5.8 years ago by Jennifer Hillman Jackson ♦ 25k

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