- galaxy-user - lists.galaxyproject.org

Re: [galaxy-user] Exome seq work flow
by Mathew Bunj 17 Mar '14

17 Mar '14

No I have not received any feedback as yet. Thanks On Friday, March 14, 2014 7:42 AM, Kristin Kernohan <kristinkernohan(a)gmail.com> wrote: Hi did anyone answer this? Id be curious to know as well thanks Kristin On Thu, Mar 13, 2014 at 10:22 PM, Mathew Bunj <mathewbunj(a)yahoo.com> wrote: I was wondering if Galaxy has any work flow for calling mutations in Exome seq and then annotating. Alignment can be done by BWA. > > >Thanks > > >Mathew >___________________________________________________________ >The Galaxy User list should be used for the discussion of >Galaxy analysis and other features on the public server >at usegalaxy.org. Please keep all replies on the list by >using "reply all" in your mail client. For discussion of >local Galaxy instances and the Galaxy source code, please >use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > >To manage your subscriptions to this and other Galaxy lists, >please use the interface at: > > http://lists.bx.psu.edu/ > >To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ >

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Unsubscribe
by Elvio Pederzolli 14 Mar '14

14 Mar '14

Hi there can you please unsubscribe me from all Galaxy lists please Thank you Elvio Pederzolli Sent from my iPad

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Re: [galaxy-user] Data Uploading through FTP
by Martin Čech 14 Mar '14

14 Mar '14

Scott: 15GB file is a candidate for a FTP upload because web browsers can't usually handle this size. FTP server address is usegalaxy.org and credentials are the same you use for Galaxy (you have to use some other client outside of web browser to connect to this FTP server and upload this large file successfully e.gg FileZilla). After you finish uploading your file there you will see it in the upload tool (Get Data / Upload File) on Galaxy (when logged in). Then you will be able to start using it in history. There is an awesome screencast that shows the full process here: http://vimeo.com/75938324 Martin On Fri, Mar 14, 2014 at 1:48 PM, Scott Tighe <scott.tighe(a)uvm.edu> wrote: > Martin > > One other thing. I believe you are incorrect about uploading using the > usegalaxy.org page with a 15 gb file. That I believe that is a mistake by > the Galaxy team. Maybe a clear tutorial on how to upload a 15gb file would > be nice. > > Thanks Again > > Scott > > > > Scott Tighe Senior Core Laboratory Research Staff Advanced Genome > Technologies Core NextGen Sequencing/Flow Cytometry University of Vermont > and Vermont Cancer Center 149 Beaumont ave Health Science Research Facility > 303/305 Burlington Vermont 05405 802-656-2482 (AGTC)On 3/14/2014 12:52 PM, > Martin Čech wrote: > > Hello Scott, > > there is no 'new Galaxy' that has changed the way upload works. If you > were able to upload files before the February release just follow the same > path. The only thing that evolved is that we added another way to upload > files that we are planning to replace the old one with - but that will > happen in the future. > > So to reiterate once more: You can use the 'old upload' that is intact > under Get Data / Upload File on the usegalaxy.org server if you have > trouble using the new one. > > If you have trouble using the new one please post a specific question > about it. > > Please do not reply to other threads with an unrelated question. > > Thank you > > Martin > > > > > On Fri, Mar 14, 2014 at 11:24 AM, Scott Tighe <scott.tighe(a)uvm.edu> wrote: > >> >> Hi Galaxy List >>> >>> If anybody has some insight as to how to upload data to the new Galaxy, >>> I sure would enjoy hearing the trick. >>> >>> Scott >>> >>> Scott Tighe >>> Senior Core Laboratory Research Staff >>> Advanced Genome Technologies Core >>> NextGen Sequencing/Flow Cytometry >>> University of Vermont and Vermont Cancer Center >>> 149 Beaumont ave >>> Health Science Research Facility 303/305 >>> Burlington Vermont 05405 >>> 802-656-2482 (AGTC) >>> >>> On 3/14/2014 10:25 AM, Jennifer Jackson wrote: >>> >>>> Hi Elvio, >>>> >>>> Peter is correct - you can manage any list membership through the >>>> mailman web pages. >>>> >>>> I found you only on this list and unsubscribed you. If you want to >>>> instead consider the galaxy-announce mailing list (low volume, general >>>> project updates), links for how to sign up are on this wiki: >>>> https://wiki.galaxyproject.org/MailingLists >>>> >>>> Best, >>>> >>>> Jen >>>> Galaxy team >>>> >>>> On 3/14/14 2:58 AM, Elvio Pederzolli wrote: >>>> >>>>> Hi there can you please unsubscribe me from all Galaxy lists please >>>>> >>>>> Thank you >>>>> >>>>> Elvio Pederzolli >>>>> >>>>> Sent from my iPad >>>>> ___________________________________________________________ >>>>> The Galaxy User list should be used for the discussion of >>>>> Galaxy analysis and other features on the public server >>>>> at usegalaxy.org. Please keep all replies on the list by >>>>> using "reply all" in your mail client. For discussion of >>>>> local Galaxy instances and the Galaxy source code, please >>>>> use the Galaxy Development list: >>>>> >>>>> http://lists.bx.psu.edu/listinfo/galaxy-dev >>>>> >>>>> To manage your subscriptions to this and other Galaxy lists, >>>>> please use the interface at: >>>>> >>>>> http://lists.bx.psu.edu/ >>>>> >>>>> To search Galaxy mailing lists use the unified search at: >>>>> >>>>> http://galaxyproject.org/search/mailinglists/ >>>>> >>>> >>>> >>> ___________________________________________________________ >>> The Galaxy User list should be used for the discussion of >>> Galaxy analysis and other features on the public server >>> at usegalaxy.org. Please keep all replies on the list by >>> using "reply all" in your mail client. For discussion of >>> local Galaxy instances and the Galaxy source code, please >>> use the Galaxy Development list: >>> >>> http://lists.bx.psu.edu/listinfo/galaxy-dev >>> >>> To manage your subscriptions to this and other Galaxy lists, >>> please use the interface at: >>> >>> http://lists.bx.psu.edu/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> >>> http://galaxyproject.org/search/mailinglists/ >>> >> >> ___________________________________________________________ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.org. Please keep all replies on the list by >> using "reply all" in your mail client. For discussion of >> local Galaxy instances and the Galaxy source code, please >> use the Galaxy Development list: >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> To manage your subscriptions to this and other Galaxy lists, >> please use the interface at: >> >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> >> http://galaxyproject.org/search/mailinglists/ >> > > >

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Exome seq work flow
by Mathew Bunj 13 Mar '14

13 Mar '14

I was wondering if Galaxy has any work flow for calling mutations in Exome seq and then annotating. Alignment can be done by BWA. Thanks Mathew

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adding danrer7 as a reference genome for tophat2
by Elwood Linney 12 Mar '14

12 Mar '14

Can you add danrer7 as a reference genome for tophat2 for online Galaxy? Its there for tophat for Illumina. Elwood Linney

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Re: [galaxy-user] File upload
by Jennifer Jackson 12 Mar '14

12 Mar '14

Hi Scott, I am sorry that you have been having problems - and hope that I can help. I just tested FTP right now - and it is working for me. My guess is that the server name being entered is incorrect. You want this to be "usegalaxy.org" (not "use_*r*_galaxy.org") for the main public site (or be whatever the base url is for the other public servers, that are supporting FTP, you may be using). On any server, this is generally noted on the 'Upload File' tool itself, in the FTP section paragraph. This is the section for the public server: The window on this tool is only appropriate for two types of upload functions, either typing in text or entering a remote URL where data is available. This remote URL could be to a FTP server, but the process is different from loading local data (on your own computer) via FTP to the Galaxy server. The video (also linked from the wiki) for this tool demonstrates all four methods for loading data. The first method is a basic browser upload of a small file - which seems to be what you are asking about - how can I help more with this part? http://vimeo.com/galaxyproject/upload For deleting data, you can either delete individual datasets or complete histories. Which are you having trouble with? There are two videos on this wiki about datasets/histories, but it sounds like they are not covering the part you need to know. If you want to provide more details, I can try to help. https://wiki.galaxyproject.org/Learn/Managing%20Datasets The server has been problematic this week, due to circumstances out of our direct control, so if you had problems earlier, trying again is most likely a good first pass solution. You can follow our Twitter feed for updates about Main @galaxyproject - posted on our wiki here: https://wiki.galaxyproject.org/Galaxy%20on%20Twitter Usability matters, so helping you to get these operations working will probably help others as well. And I can add into our documentation what is unclear or missing. Plus most of our wiki is open - community members are encouraged to add new pages or comments to fill in/share help ideas. Thanks! Jen Galaxy team On 3/12/14 2:11 PM, Scott Tighe wrote: > Jennifer > > It is a total mystery how to get data uploaded. Just like it is a > total mystery how to delete it. Spent an hour and a half reviewing > your tutorials and trying FTP. The FTP does not work anymore and if > you put the term usergalaxy.org in to the FTP window, it does not like > that. The tutorials were not useful and appear to be based on FTP. > Maybe you could do a tutorial on how exactly to upload like 10gB. Arrggg > > Thanks > Scott Tighe > Senior Core Laboratory Research Staff > Advanced Genome Technologies Core > NextGen Sequencing/Flow Cytometry > University of Vermont and Vermont Cancer Center > 149 Beaumont ave > Health Science Research Facility 303/305 > Burlington Vermont 05405 > 802-656-2482 (AGTC) > On 3/12/2014 1:17 PM, Jennifer Jackson wrote: >> Hi Scott, >> >> Is the 'Get Data -> Upload File' tool no longer functioning for you? >> Can I help with using Main or is this on a local/cloud instance that >> needs to be set up? >> https://wiki.galaxyproject.org/Support#Loading_data >> >> It is correct that the addition upload methods via the "Load Data" >> process - found at the top of the tool panel - are not included in >> our tutorials/vidoes yet. This is very new set of methods (first was >> placed on Main at the end of January) and may still undergo some >> changes. We expect this to stabilize near-term and then be >> documented. Both tools will continue to co-exist. >> >> If there are any usage question right now (you or others) please let >> us know and we can help. The functions are either the same or very >> similar to the 'Upload File' tool, just presented in a different >> pop-up interface, plus now include convenience/feedback features. >> >> Thanks! >> >> Jen >> Galaxy team >> >> On 3/12/14 12:57 PM, Scott Tighe wrote: >>> For all users: >>> >>> The tutorial on uploading data is incorrect. I do not think they >>> have updated "how to upload data" yet. >>> >>> Scott >>> Scott Tighe >>> Senior Core Laboratory Research Staff >>> Advanced Genome Technologies Core >>> NextGen Sequencing/Flow Cytometry >>> University of Vermont and Vermont Cancer Center >>> 149 Beaumont ave >>> Health Science Research Facility 303/305 >>> Burlington Vermont 05405 >>> 802-656-2482 (AGTC) >> >> -- >> Jennifer Hillman-Jackson >> http://galaxyproject.org > -- Jennifer Hillman-Jackson http://galaxyproject.org

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Enquiry regarding the working of Galaxy
by Sathya 12 Mar '14

12 Mar '14

Now the galaxy main server is not working. I would like to know how long it will take for galaxy to work again. -- With regards, Sathya.B

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Update from server failed several times
by Meike.Latz＠mdc-berlin.de 12 Mar '14

12 Mar '14

Hello, I deleted some files, because I reached 100% of the data volume I could use; my actual volume is 76 GB. I'm waiting now for an update from the server, that I reduced the data volume and can continue with my analysis. But I got a red note on the history for several times, that the update failed and that I should contact you, when it does so. What could I do now, to get an update from the server? Thanks in advance! Best, Meike

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Re: [galaxy-user] can galaxy analyze SOLiD XSQ dataset except csfasta/qual data?
by Chandran, Uma 12 Mar '14

12 Mar '14

Are there mappers for SoLiD 5500 on Galaxy? If so, do they take csfasta files as input? Thanks Uma Chandran

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Cuffdiff output
by Malik, Shivani 12 Mar '14

12 Mar '14

Hi, I have a question about interpreting the cuffdiff data and how to pick up significant genes. I have genes which show ~8 fold change between 2 conditions: eg from FPKM of 0.08 to 28 and yet they are not significant. Is there is threshold of FPKM below which Cuffdiff does not consider it an FPKM to be valid and hence significance in "no"? What downstream analysis should I use to extract a meaningful list of genes from the Cuffdiff data? Also, I filtered out FPKMs which were below 5 in both conditions? Is that reasonable? Thanks Shivani

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