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 t

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 loca

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 t

[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

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) f

[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 a

[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 t

[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 fro