Re: [galaxy-user] Cuffdiff no without replicates
On Wed, Oct 3, 2012 at 9:11 PM, i b ibse...@gmail.com wrote: Dear all, how reliable is running Cuffdiff without replicates? e.g.one samples agains another one? Is it statistically makign any difference when using replicates? Seqanswers might be a better place to ask this very interesting technical question that goes way beyond Galaxy... My 2c: Statistically speaking, sequencing and biology are both noisy. Replicates provide information about non-experimental (technical and biological) variation. That variation is usually not the variation you are looking for, but if you want to remove it, you have to model it and that requires information from replicates (or really good guesswork). In some situations (eg extreme experimental conditions), I'm sure you'll find biologically meaningful signal without them but in my experience, they can really help to decrease non-experimental noise, particularly where the experimental condition induces only subtle changes in transcript abundance. You could always analyse a data set with replicates and compare the results with and without those replicates yourself to see what happens - it would be a nice paper I'm sure. Thanks, ib ___ 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/
Re: [galaxy-user] Cuffdiff no without replicates
On Wed, Oct 3, 2012 at 7:35 AM, Ross ross.laza...@gmail.com wrote: On Wed, Oct 3, 2012 at 9:11 PM, i b ibse...@gmail.com wrote: Dear all, how reliable is running Cuffdiff without replicates? e.g.one samples agains another one? Is it statistically makign any difference when using replicates? Seqanswers might be a better place to ask this very interesting technical question that goes way beyond Galaxy... My 2c: Statistically speaking, sequencing and biology are both noisy. Replicates provide information about non-experimental (technical and biological) variation. That variation is usually not the variation you are looking for, but if you want to remove it, you have to model it and that requires information from replicates (or really good guesswork). In some situations (eg extreme experimental conditions), I'm sure you'll find biologically meaningful signal without them but in my experience, they can really help to decrease non-experimental noise, particularly where the experimental condition induces only subtle changes in transcript abundance. You could always analyse a data set with replicates and compare the results with and without those replicates yourself to see what happens - it would be a nice paper I'm sure. A bit off-topic, but you might take a look here: http://www.ncbi.nlm.nih.gov/pubmed/21747377 In short, one needs replication in biology, regardless of the technology used. In particular, one would never suggest running a microarray experiment without replicates; one should follow approximately the same rules for sequencing (and sequence data analysis). Sean Thanks, ib ___ 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/ ___ 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/
[galaxy-user] blast tools on free public server
We're using the free public Galaxy server (main.g2.bx. psu.edu). We uploaded a genome FASTA sequence via ftp, and want to do BLAST searches (e.g., tblastn) against protein sequences that we've also uploaded to Galaxy, as well as on NCBI. BLAST tools don't show in the tools column, or when entered in the search box. Google searches on 'BLAST in Galaxy' bring up pages on 'wrappers' and xml, and we're but humble biologists. Can anyone please explain (simply, presuming no knowledge of wrappers, perl, python, java, scripts, xml, etc. on our part) how we can do this? Thank you. John D ___ 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/
Re: [galaxy-user] Cannot find upload options
Hello Matina, This wiki explains how to load data libraries as an admin: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries Best, Jen Galaxy team On 10/3/12 7:15 AM, Matina Fragkogianni wrote: Hello, I have an instance of Galaxy locally and I'm trying to upload a dataset. I have administrator privileges and I have already created a data library. The problem is that I want to upload a directory of files into Galaxy but in the drop-down menu (Upload option:) I have only two options 1) upload files (where i can upload only one file at a time) 2) import dataset from current history. I don't have the other options show on the wiki. Do you have any idea what the problem might be? I've downloaded the latest version as instructed using this command. ( hg clone https://bitbucket.org/galaxy/galaxy-dist/) Kind Regards, Matina ___ 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/ -- Jennifer Jackson http://galaxyproject.org ___ 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/
Re: [galaxy-user] blast tools on free public server
On Wed, Oct 3, 2012 at 3:54 PM, John DeFilippo defilippo.j...@gmail.com wrote: We're using the free public Galaxy server (main.g2.bx. psu.edu). We uploaded a genome FASTA sequence via ftp, and want to do BLAST searches (e.g., tblastn) against protein sequences that we've also uploaded to Galaxy, as well as on NCBI. BLAST tools don't show in the tools column, or when entered in the search box. Google searches on 'BLAST in Galaxy' bring up pages on 'wrappers' and xml, and we're but humble biologists. Can anyone please explain (simply, presuming no knowledge of wrappers, perl, python, java, scripts, xml, etc. on our part) how we can do this? Thank you. John D Offering BLAST searches is potentially quite computationally expensive, so for the moment at least the BLAST+ suite is not made available on the public Galaxy hosted by Penn State (with the exception of the megablast function offered with four databases only). The BLAST+ wrappers are available on the Galaxy Tool Shed, and can be installed to any local Galaxy server. They can then be run on your local server (and ideally your local cluster). That's what we do. If you have a Galaxy installation at your institute/department/... ask the local Galaxy administrator about this. Regards, Peter ___ 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/
Re: [galaxy-user] blast tools on free public server
Hello John, To use all BLAST+ functions with Galaxy, a local or cloud instance is needed. The public main Galaxy instance does not host tblastn, only megablast (based on blastn) - and only for certain databases. Many biologists prefer using a cloudman instance as much of the set-up is already packaged and it does not require an investment in local hardware/servers/data tool setup. Details can be found in our wiki at: Cloudman: http://usegalaxy.org/cloud Local instance: http://getgalaxy.org The best mailing list for local or cloud instance support, should you run into issues (or just want to follow the technical threads), is galaxy-...@bx.psu.edu. http://wiki.g2.bx.psu.edu/Mailing%20Lists Hopefully this helps! Jen Galaxy team On 10/3/12 7:54 AM, John DeFilippo wrote: We're using the free public Galaxy server (main.g2.bx. psu.edu). We uploaded a genome FASTA sequence via ftp, and want to do BLAST searches (e.g., tblastn) against protein sequences that we've also uploaded to Galaxy, as well as on NCBI. BLAST tools don't show in the tools column, or when entered in the search box. Google searches on 'BLAST in Galaxy' bring up pages on 'wrappers' and xml, and we're but humble biologists. Can anyone please explain (simply, presuming no knowledge of wrappers, perl, python, java, scripts, xml, etc. on our part) how we can do this? Thank you. John D ___ 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/ -- Jennifer Jackson http://galaxyproject.org ___ 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/
[galaxy-user] Fastq-groomer help
Hello: I have this 20GB data that I have uploaded onto my history and trying to get it run thr groomer. Just the first data set was uploaded yesterday and ran groomer on it and it was not done this morning. The message indicated taht it is still waiting to be run !!! I have 57 data sets to run and would appreciate if you could inform me about how long it may take to even get started or any other suggestion to get my job done will help. Thanks so much, user name :genenart Kshama. -- Kshama Aswath Graduate Student-(PhD) Bioinformatics and computational Biology Prince Williams Campus George Mason University Manasses,VA-20110 ___ 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/
