March 2014 - galaxy-user - lists.galaxyproject.org

Help with Summary Statistics
by D. A. Cowart 23 May '14

23 May '14

Hello, I am attempting to use Galaxy to calculate the mean sequence read length and identify the range of read lengths for my 454 data. The data has already been organized and sorted by species. The format of the data is as follows: >HD4AU5D01BHBCQCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC >HD4AU5D01A093MCTCTGTCGCTCTGTCTCTCTTCTCTCTCTCTCTCTCT etc...for each species I have attempted to use the "Summary Statistics" button, however it appears to only be for numerical data and not sequence data. Is this tool/task available via Galaxy? Thank you, Dominique Cowart User name: dac330

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question history
by Liesbeth Van Rompay 01 Apr '14

01 Apr '14

Hi, Although I am occupying 91% of my space on the Galaxy platform, since Galaxy was out, I cannot access my history anymore. No error message appears. What can I do? Best regards, Liesbeth

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Job of format conversion waiting for over 5 days
by Eduardo Fox 31 Mar '14

31 Mar '14

Hello, Please I would like to know if it would be normal of a job to be queued for several days? It is a SAM to BAM conversion, and it has been waiting for over 5 days to run. I understand that the SAM file is pretty large but other similar conversions I made on the server recently were done within few minutes. Thanks! -- Eduardo G. P. Fox http://eduardofox.blogspot.com.br/ http://www.mendeley.com/profiles/eduardo-fox/

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April 2014 Galaxy Update Newsletter: GCC2014 Talk Abstracts due this Friday
by Dave Clements 31 Mar '14

31 Mar '14

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error while running Intogen.
by do kadya 29 Mar '14

29 Mar '14

Respected Sir / Ma'am, I was running Intogen using galaxy, I changes parameters name and then this error came. Can you please tell what is the meaning of this error ? Traceback (most recent call last): File "/home/ganit/galaxy_work/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 123, in prepare_job job_wrapper.prepare() File "/home/ganit/galaxy_work/galaxy-dist/lib/galaxy/jobs/__init__.py", line 702, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/home/ganit/galaxy_work/galaxy-dist/lib/galaxy/tools/__init__.py", line 2639, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/home/ganit/galaxy_work/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/home/ganit/galaxy_work/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1395998029_86_91764.py", line 100, in respond NotFound: cannot find 'fimpact'

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Globus World 2014
by Ravi K Madduri 28 Mar '14

28 Mar '14

Dear All I wanted to send a note to folks about Globus World 2014. I apologize before hand for spamming both the developer list and the users list also but I thought this may be relevant to folks on the lists. Please let me know if you have any questions. GlobusWorld is this year’s biggest gathering of all things Globus. GlobusWorld 2014 features a Using Globus Genomics to Accelerate Analysis Tutorial, and a full half day on Globus Genomicsin the main meeting, including a keynote by Nancy Cox and these accepted talks: Globus Genomics: Enabling high-throughput cloud-based analysis and management of NGS data for Translational Genomics research at Georgetown, by Yuriy Gusev, Improving next-generation sequencing variants identification in cancer genes using Globus Genomics, by Toshio Yoshimatsu Globus Genomics: A Medical Center's Bioinformatics Core Perspective, by Anoop Mayampurath Building a Low-budget Public Resource for Large-scale Proteomic Analyses, by Rama Raghavan Globus Genomics is a Globus and Galaxy based platform for genomic analysis. GlobusWorld is being held April 15-17, in Chicago. And, GCC2014 is a Silver Sponsor of GlobusWorld. -- Ravi K Madduri MCS, Argonne National Laboratory Computation Institute, University of Chicago

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Re: [galaxy-user] Trackster Error
by Jeremy Goecks 27 Mar '14

27 Mar '14

Hi Suzanne, Thanks for sharing your history. This is a file format issue on our side. We’ll get it taken care of and let you know when it’s fixed. Thanks, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University > > > On Mar 27, 2014, at 9:27 AM, Jeremy Goecks <jgoecks(a)gwu.edu> wrote: > >> Hi Suzanne, >> >> Can you share your history with me and I’ll take a look? >> >> Thanks, >> J. >> >> -- >> Jeremy Goecks >> Assistant Professor of Computational Biology >> George Washington University >> >> >> >> On Mar 24, 2014, at 5:08 PM, Suzanne Gomes <suzanneluziagomes(a)gmail.com> wrote: >> >>> Hello, >>> >>> I am trying to look at an output from Tophat using Trackster, but I keep getting the following error: >>> >>> Could not load chroms for this dbkey: dp4 >>> >>> This is not a custom dbkey - I just selected it from the list of available ones on Trackster. >>> >>> I have database/build set to: D. pseudoobscura (dp4) (dp4) for my Tophat results. >>> >>> Any ideas why this is happening and what I can do to fix it? >>> >>> Thanks >>> >>> Suzanne >>> ___________________________________________________________ >>> 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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Trackster Error
by Suzanne Gomes 27 Mar '14

27 Mar '14

Hello, I am trying to look at an output from Tophat using Trackster, but I keep getting the following error: Could not load chroms for this dbkey: dp4 This is not a custom dbkey - I just selected it from the list of available ones on Trackster. I have database/build set to: D. pseudoobscura (dp4) (dp4) for my Tophat results. Any ideas why this is happening and what I can do to fix it? Thanks Suzanne

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ftp not working
by David Matthews 27 Mar '14

27 Mar '14

Hi, I'm still not able to use ftp - keeps saying connection refused either through the command line or through cyberduck - is anyone else seeing this? Best Wishes, David. _________________________________ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 D.A.Matthews(a)bristol.ac.uk

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Question regarding storage space
by Alexandre Maia 27 Mar '14

27 Mar '14

I am using Deeptools at the main public server and was adding some files initially to test. Now I have removed all my files (hidden and unhidden) and history, but my usage is still at 38%. How can I remove all the files to have a 0%? My user name is alexandre.gaspar.maia(a)gmail.com Thanks. A

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upload data to galaxy using terminal
by do kadya 26 Mar '14

26 Mar '14

Hi, Can I upload data (mostly link the data) using terminal ? MuSiC 2 tool integration is not available in their website nor in tool shed. MuSiC 2 creates folder and files by itself, which is hard to track by Galaxy. So is there any way to link files to galaxy current work space so that I can link those distracted files which are created by MuSiC 2. ex: if you run music2 bmr calc-bmr file_of_input output is 3 files, ./file1.txt ./folder1/file2.txt ./folder2/file3.txt we can not mention that we need this output filename or save file at specific location, we can not give this option. Galaxy will not able to track this output, hence i have to do it manually. So is it possible to upload this files manually by terminal ? Waiting for positive reply. Thank You - Chetan

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GCC2014 Early Registration and Abstract Submission are now OPEN!
by Dave Clements 25 Mar '14

25 Mar '14

Hello all, *We are pleased to announce that Early Registration <https://wiki.galaxyproject.org/Events/GCC2014/Register> and Talk and Poster Abstract Submission <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts> are now open for the 2014 Galaxy Community Conference (GCC2014) <https://wiki.galaxyproject.org/Events/GCC2014>.* GCC2014 <https://wiki.galaxyproject.org/Events/GCC2014> will be held at the Homewood Campus<http://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewo…>of Johns Hopkins University <http://jhu.edu>, in Baltimore, Maryland<http://visitors.baltimorecity.gov/>, United States, from June 30 through July 2, 2014. GCC2014<https://wiki.galaxyproject.org/Events/GCC2014>starts with a Training Day <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> featuring four *five* parallel tracks, each with three, two and half hour long workshops. There are 13 different topics spanning the full Galactic spectrum of topics. Take a look!<https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> *Early registration <https://wiki.galaxyproject.org/Events/GCC2014/Register>* is now open. Register early and *avoid paying 70% more for regular registration costs.* Early registration is very affordable, with combined registration (Training Day <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> + main meeting) starting at $140 for post-docs and students. Registration is capped this year at 250 participants, *and we expect to hit that limit*. Registering early assures you a place at the conference and also a spot in the Training Day workshops you want to attend. You can also book affordable conference housing at the same time you register. See the conference Logistics page<https://wiki.galaxyproject.org/Events/GCC2014/Logistics>for details on this and other housing options. *Abstract submission <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts>* for both oral presentations and posters is also open. Abstract submission for oral presentations closes April 4, while poster submission closes April 25. Poster authors will be notified of acceptance status within two weeks of submission, while presentation authors will be notified no later than May2. *Please consider presenting your work. If you are dealing with big biological data, then this meeting wants to hear about your work.* The *GigaScience <http://www.gigasciencejournal.com/>* "Galaxy: Data Intensive and Reproducible Research" series announced for the last conference has published its first papers<http://www.gigasciencejournal.com/series/Galaxy>, *and is continuing to take submissions for this year's meeting and beyond*. BGI is also continuing to cover the article processing charges until the end of the year, and for more information see their latest update<http://blogs.biomedcentral.com/gigablog/2014/02/06/rewarding-reproducibilit…>. Thanks, and hope to see you in Baltimore! The GCC2014 Organizing Committee<https://wiki.galaxyproject.org/Events/GCC2014/Organizers> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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Output file to history
by Sebastian Luna Valero 21 Mar '14

21 Mar '14

Dear All, I am trying to add a new tool in Galaxy and I have the following problem. Let me explain a simplified example. Let's imagine that my script works from CLI as follows: python script.py --input "input-file" --pattern "output-pattern" After processing "input-file", the script writes several output files and their name is given according to "output-pattern". The number of output files depends on the content of "input-file". The output files are written to the current working directory where script.py is located. In the simplest scenario, I get only one output file in the working directory. My problem is that I would like to see the output files in Galaxy's history without modifying the CLI interface. To solve this problem, I have looked at the wiki page: https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number… and the email here: http://dev.list.galaxyproject.org/Multiple-output-files-do-not-appear-in-hi… However, I think that mine is a different scenario. I do not want to add new output parameters in the CLI. I would like Galaxy to bring these output files to my history without modifying the CLI options, is that possible? Many thanks in advance for your help! Best regards, Sebastian.

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Usegalaxy.org network upgrade this Saturday
by Dave Clements 18 Mar '14

18 Mar '14

Hello all, Access to all TACC resources and services, including UseGalaxy.org<https://usegalaxy.org/>, will be unavailable between 9 a.m. - 5 p.m. (US Central Time) on Saturday, March 22. TACC staff will be performing an upgrade to the networking infrastructure. During this outage, users are encouraged to use the *50+ other public Galaxy servers <https://wiki.galaxyproject.org/PublicGalaxyServers>* that won't be affected by this upgrade. We apologize for any inconvenience this may cause you. Thanks, Dave C -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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please unsubscribe
by Bogdan Tanasa 17 Mar '14

17 Mar '14

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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 14 Mar '14

14 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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