Re: [galaxy-user] Read_group_tracking files are not enough for cummerbund visualisations on replicates?
Hello Elihu, The tool was just recently upgraded to include these files. https://trello.com/c/FdUYdbIn The update will be available in the Tool Shed then updated on the main public server at (or possibly before) the next stable release. Other pending updates to the tool suite include adding these additional features. https://trello.com/c/lIdpOZ88 https://trello.com/c/U7nceKdj Good question! Sometimes the updates are because the tool itself changed, sometimes they are simply updates to add in more features as they are requested/needed. The Trello cards will usually note the history and any comments. Jen Galaxy team On 11/20/13 6:22 AM, Aranday Cortes, Elihu wrote: Hi, Cuffdiff in Galaxy produces "read_group_tracking" files. However, I wonder if these files are enough when using 'replicates=T' in cummeRbund or I also need "read_groups.info" and "run.info" files in myDir. I've tried 'replicates(cuff)' with the 'read_group_tracking' files in my directory and I get back an empty set, means that cummerbund is not using replicates (or I'm doing something wrong!). At this time I don't see other option that run cuffdiff locally. At least you have any suggestion or advice about how I can get 'info.files' from Galaxy. Any particular reason why Cuffdiff output files in Galaxy are not ALL the files described in the manual tool? Thanks for you help. Elihu ___ 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/ -- Jennifer Hillman-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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Cufflinks returned 0 value in all RPKMs
Hello, If the data is RNA from rat, then you will want to be using Tophat instead of Bowtie. Otherwise the data will not be mapped as spliced the results will be off in many ways (the fragments counts are a small symptom of a larger problem). You can use 'Tophat for SOLiD' on a suitable local or cloud Galaxy instance. It is available on the Test server, but tools are not supported here (we test/break things!) and the quotas are just 10G with an account. But maybe is a place to do a small trial run before committing to a cloud server. http://getgalaxy.org http://usegalaxy.org/cloud http://usegalaxy.org/toolshed More about RNA-seq is in our wiki and public server, including link-outs and tutorials, you can get started here: Example ? RNA-seq analysis tools: http://wiki.galaxyproject.org/Support#Interpreting_scientific_results See RNA-seq examples: http://wiki.galaxyproject.org/Learn#Other_Tutorials Best, Jen Galaxy team On 11/20/13 6:09 AM, Ly, Dao wrote: Hi I have been trying to analyze a rat Solid SRA but I encountered a problem: cufflinks gave me 0 RPKM in all genes. Here is my workflow 1. Get data with EBI SRA: sent the fastaq file directly to galaxy 2.Fastaq groomer 3.Mapped with bowtie for Solid (paire-ended) with the built- in index rat rn5 as reference genome 4.Sam to Bam the bowtie mapping result 5.Cufflinks the bam file All RPKMs of gene expression and transcript expression have a 0 value even thought the RPKM status is OK. I used default setting for all jobs. Am I missing something? Any help, suggestion will be greatly appreciated. Thank you very much Best regards Dao ___ 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/ -- Jennifer Hillman-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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Quantmap output issue (chemical names are truncated and cannot be differentiable from each other)
Hi Jui-Hua, You have reached the public Main Galaxy user help list. But my guess is that you are trying to reach the PredPharmTox public Galaxy instance, for help with their specific tools: http://wiki.galaxyproject.org/PublicGalaxyServers?highlight=%28QuantMap%29#PredPharmTox I wasn't able to find contact information on the server itself or our wiki, but you could start with the publication authors for the tools, listed as contacts after the abstract here: http://bioinformatics.oxfordjournals.org/content/early/2013/07/04/bioinformatics.btt390.full.pdf If we have more specific contact information to share (is possible!), we'll add to the thread, Good luck! Jen Galaxy team On 11/20/13 3:33 PM, Hsieh, Jui-Hua (NIH/NIEHS) [E] wrote: Hi, I have submitted chemicals to the QuantMap. The chemicals are successfully prepared by the "QuantMap Prep" and run by "QuantMap server". However, in the output files (dendrogram as well as the cluster information), all of the chemical names are truncated. Thus, some chemicals with identical truncated names cannot be differentiated from each other. I wonder if CIDs or full chemical names can be reported as well. Thank you, Jui-Hua ___ 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/ -- Jennifer Hillman-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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] Quantmap output issue (chemical names are truncated and cannot be differentiable from each other)
Hi, I have submitted chemicals to the QuantMap. The chemicals are successfully prepared by the "QuantMap Prep" and run by "QuantMap server". However, in the output files (dendrogram as well as the cluster information), all of the chemical names are truncated. Thus, some chemicals with identical truncated names cannot be differentiated from each other. I wonder if CIDs or full chemical names can be reported as well. Thank you, Jui-Hua ___ 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/
Re: [galaxy-user] compute an expression on every row question
Hi Tobias, The "Compute" tool does output just one column of data. The parenthesis are problematic to get rid of, so the starting and ending values would need to be disposable. Then you could break up this column with the tool "Convert delimiters to TAB" (commas and spaces can be converted) followed by "Cut" to just pull out the ones that you want (watch out for double tabs - or remove them if really wanted with the tool " Condense consecutive characters"). And you are correct, using a workflow to add the columns iteratively is another option. The good thing about a workflow is that once created, you can run it as if it was a single "tool", placing it in the tool menu and hiding intermediate output datasets. Either of these could become a workflow. There is the tool "Arithmetic Operations on tables" on the Test server (https://test.galaxyproject.org/), but this would involve creating a new separate file that would be about as much work as the the others. I didn't see any obvious solutions in the Tool Shed for use in a local instance (this type of simple operation should be fine on a basic laptop install), but this is something you could also review. http://usegalaxy.org/toolshed Hopefully one of these options will work out for you, even if not a single step, Jen Galaxy team On 11/18/13 9:59 PM, Tobias Hohenauer wrote: Hello, I am looking for the right way to do a computation using "text manipulation, compute an expression on every row". I have a table consisting of 20 columns and about 15.000 rows. Column 1 is my untreated or control and I would like to normalize every other column to this control by simple division. As a result I would like to obtain a table in which column 1 is set to a value of 1 for every row, and the corresponding values in the other columns resulting from column x / column 1. I tried something like c2/c1,c3/c1,c4/c1... on a small testfile but that results in all normalized values being put into one column in brackets rather than being put into individual columns. What would be the right parameters? I also thought about creating a workflow consisting of successive divisions of the columns but that feels rather complicated. Is there an easier way? Any help would be much appreciated! Best, Tobias -- Jennifer Hillman-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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] Read_group_tracking files are not enough for cummerbund visualisations on replicates?
Hi, Cuffdiff in Galaxy produces "read_group_tracking" files. However, I wonder if these files are enough when using 'replicates=T' in cummeRbund or I also need "read_groups.info" and "run.info" files in myDir. I've tried 'replicates(cuff)' with the 'read_group_tracking' files in my directory and I get back an empty set, means that cummerbund is not using replicates (or I'm doing something wrong!). At this time I don't see other option that run cuffdiff locally. At least you have any suggestion or advice about how I can get 'info.files' from Galaxy. Any particular reason why Cuffdiff output files in Galaxy are not ALL the files described in the manual tool? Thanks for you help. Elihu ___ 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/
[galaxy-user] Cufflinks returned 0 value in all RPKMs
Hi I have been trying to analyze a rat Solid SRA but I encountered a problem: cufflinks gave me 0 RPKM in all genes. Here is my workflow 1.Get data with EBI SRA: sent the fastaq file directly to galaxy 2. Fastaq groomer 3. Mapped with bowtie for Solid (paire-ended) with the built- in index rat rn5 as reference genome 4. Sam to Bam the bowtie mapping result 5. Cufflinks the bam file All RPKMs of gene expression and transcript expression have a 0 value even thought the RPKM status is OK. I used default setting for all jobs. Am I missing something? Any help, suggestion will be greatly appreciated. Thank you very much Best regards Dao ___ 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/
[galaxy-user] Implement GATK tool "Callable Loci" in Galaxy?
Hi all, First of all, thank you again for all your efforts to develop a project like Galaxy, that makes leading-edge bioinformatic tools available for non-bioinformaticians and wet-lab biologists like me ! I am using GATK Unified Geneotyper through the Galaxy main server to analyze variations from whole-genome re-sequencing data. I have read in the GATK documentation that there is a tool called "CallableLoci", that gives a .bed file of the genome indicating specifically which base where callable or not by Unified Genotyper (UG), using different criteria such as read depth, base quality, mapping quality. The log & metrics files generated by UG in Galaxy give the general statistics of callable loci, but there is no such a file giving a detailed information of the eligibility of each base. Right now I am using the tool "depth of coverage on BAM file" to get an idea of this information, but it's only partial since it doesn't take into account all the parameters used by UG to consider a locus callable (notably base quality and mapping quality). Do you think it would be possible to implement the "CallableLoci" tool in Galaxy? Would someone propose me an alternative to get this precious information on which areas of the genome are considered callable ? Thanks for your help/advice, Fabrice ___ 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/
