[galaxy-user] Bismark Error: Data table named 'bismark_bs_indeces' is required by tool but not configured.
Hi all, I am seeing this error while clicking on Bismark in Galaxy. I got the Bismark for galaxy tool shed. I tried to get another bismark wrapper developed by Bjoern. I didnt know how to download that. What's the error? Thanks ___ 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] Bismark Error: Data table named 'bismark_bs_indeces' is required by tool but not configured.
Hello Sachit, It looks like you installed this from the test tool shed since it is not available on the main tool shed. Assuming I've located the repository you installed, it looks like you'll have to manually add the following entry into your tool_data_table_conf.xml file. This should have been done automatically for you when you installed the repository, but I'm not sure why it didn't. Maybe you're running an older version of Galaxy that doesn't include this automated feature. Greg Von Kuster !-- Locations of all bismark converted bs-seq references -- table name=bismark_bs_indeces comment_char=# columnsvalue, dbkey, name, path/columns file path=tool-data/bismark_bs_indeces.loc / /table On Nov 29, 2012, at 4:41 AM, Sachit Adhikari wrote: Hi all, I am seeing this error while clicking on Bismark in Galaxy. I got the Bismark for galaxy tool shed. I tried to get another bismark wrapper developed by Bjoern. I didnt know how to download that. What's the error? Thanks ___ 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] filter for +/- 2-fold difference in expression levels
Hey guys, I have my Cuffdiff output and I was trying to figure out how to get the data I need. I am interested in the outputs Transcript and Gene differential expressed. Does anyone know how to filter for +/- 2-fold difference in expression levels? Thank you Giuseppe Ianiri, Ph.D. Division of Cell Biology and Biophysics School of Biological Sciences 5100 Rockhill Road University of Missouri-Kansas City Kansas City, MO 64110 Email: iani...@umkc.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] Data/history/user export and import
Dear all, Would it be possible somehow to not only export a single history of a user (to file) but also all histories of a user in one go. Or even all user-bound histories/settings and such? I would like to import them into another galaxy instance (basically from our internal development (galaxy_central) server to our public production (galaxy-dist) server), but going over them one-by-one will be a laborious task. Both instances are up-to-date. I do have admin access to both the galaxy instances (as we own them) so admin bound tools and/or possibilities from commandline would be suitable as well. Since I am unsure where it fits in the user-list or dev-list I cross-posted to both (sorry). Thanks in advance! Alex ___ 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] dataset not visible
Dear, I am working on the free public server of Galaxy for almost a week. When I opened the galaxy server this morning, my datasets were not visible. I have tried show hidden datasets or show deleted datasets, but nothing changed. How can I make my datasets visible? Thanks, Kind regards, Ilse --- [cid:image001.png@01CDCE11.0DF442D0] http://www.ugent.be/fw/en/research/pharmaceutical-analysis/pmicro http://www.sociomicrobiology.ugent.be/ - inline: image001.png___ 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] Stitch Gene blocks return empty result???
Hello, The regions in your BED file appear to be representing non-coding transcripts, which is why there is no output using this specific tool. A better choice would be the tool Stitch MAF blocks. Hopefully this helps. Next time, please only post to a single list. For usage questions like this one, the galaxy-u...@bx.psu.edu mailing list is best. http://wiki.galaxyproject.org/Support#Mailing_Lists Thanks! Jen Galaxy team On 11/29/12 4:03 AM, 张坤山 wrote: Hi all, I trying to stitch some MAF from bed12 file using Stitch Gene blocks. Galaxy successfully recognized my BED file and finished stitch, but no sequence in the result. My BED file is like: chr1 14662810 14707010 TCONS_7949 0 - 14707010 14707010 0 5 229,139,106,162,77, 0,4387,4975,8271,44123, chr1 84928679 84942052 TCONS_00027714 0 + 84942052 84942052 0 4 64,173,111,398, 0,1330,12292,12975, chr1 91200237 91254779 TCONS_00030473 0 - 91254779 91254779 0 3 285,177,104, 0,52636,54438, I choose 36 mammals to stitch blocks. Galaxy gives me result like: mm9.TCONS_7949 hg19.TCONS_7949 panTro2.TCONS_7949 No sequence in result.What happen?? ** Kunshan ___ 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] Clip doesn't see my FASTQ file
Hi Steve, Are you still having problems with this tool? And the datatype is assigned as .fastq or .fastqsanger? If you would like to send a shared link to the history, I can take a look and give feedback. From the history panel, use: Options (gear icon) - Share or Publish - generate a share link - then copy that into a return email to just me (to keep your data private). Best, Jen Galaxy team On 11/28/12 4:08 AM, Stephen Eacker wrote: Hello, I'm using Galaxy on the PSU server. I uploaded a FASTQ file that I want to run the Clip Adapter Tool, but this tool does not see my FASTQ file in the 'Library to clip' drop-down. I have successfully run FASTQC on this same file, so Galaxy does properly see this file as being a FASTQ file. Any thoughts? thanks, Steve Stephen Eacker, Ph.D. Research Associate Dawson Lab Institute for Cell Engineering Johns Hopkins Medical Institute (443) 287-5605 seack...@jhmi.edu mailto:seack...@jhmi.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/ -- 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] filter for +/- 2-fold difference in expression levels
Thank you Jennifer. I just start working with these things, so I am wondering which minimal value of FPKM I should use in the filter tool. Do you have an advice or an example that I could look at? Thank you Giuseppe Ianiri, Ph.D. Division of Cell Biology and Biophysics From: Jennifer Jackson [j...@bx.psu.edu] Sent: Thursday, November 29, 2012 10:51 AM To: Ianiri, Giuseppe Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] filter for +/- 2-fold difference in expression levels Hello Giuseppe, Fold is included in the Cuffdiff output. Section Differential expression tests, first file, column #9. http://cufflinks.cbcb.umd.edu/manual.html A tool like Filter and Sort - Filter could be used to subset specific values. Hopefully this helps, Jen Galaxy team On 11/29/12 5:35 AM, Ianiri, Giuseppe wrote: Hey guys, I have my Cuffdiff output and I was trying to figure out how to get the data I need. I am interested in the outputs Transcript and Gene differential expressed. Does anyone know how to filter for +/- 2-fold difference in expression levels? Thank you Giuseppe Ianiri, Ph.D. Division of Cell Biology and Biophysics School of Biological Sciences 5100 Rockhill Road University of Missouri-Kansas City Kansas City, MO 64110 Email: iani...@umkc.edumailto:iani...@umkc.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/ -- 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] trim adapters and other
Hi, all! I have a maybe naive question that might be not so related to Galaxy usage. So I got the RNA seq data from Illumina Hiseq. Do I need to get rid of the adapter manually? If so, is it clip adapter that I should use? It should only have one adapter sequence or maybe more than one? And the adapters should be in both sides or just one side? Then my next question is from the Illumina sequencing principle, they use adapter to amplify sequence and primers to do base call, so sequence data should not have any adapter information, is it right? In my case, my small RNA data are all 75bp sequences, which is weird to me because my expectation is a bundle of sequence ranging from 20-30bp. Have any of your guy encountered such problems? Thanks in advance! Zhiqiang ___ 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] Cuffdiff tracking file does not report all genes and trancrips from reference annotation?
Hi, Galaxy user. I ran into a problem when using Cuffdiff 1.2.1 in Galaxy local instance to check differential expressed genes in my samples. I have 3 normals and 6 cancers samples, I did the following: - After tophat for each samples, run cufflink with refseq annotation which has 25266 genes and 43091 transcripts - cuffmerge all cufflink outputs contains 58112 lines - run cuffdiff with 3 normals as triplicate and compare to each cancer sample. Suprisingly, I fould out that the tanscripts tracking file, gene tracking, CDS tracking only has 2000 genes and 4000 transcripts. So the cufflink only compare 2000 genes and 4000 transcripts between samples. The question I want to ask here is that *why are the rest of the genes and transcripts not being tested and included in the tracking files?* Do you know what cause this kind of problem? Thanks, Wei -- Wei Liao Research Scientist, Brentwood Biomedical Research Institute 16111 Plummer St. Bldg 7, Rm D-122 North Hills, CA 91343 818-891-7711 ext 7645 ___ 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] filter for +/- 2-fold difference in expression levels
Hi Guiseppe, This RNA-seq tutorial has an example walk-through using these tools plus links to documentation sources that can help guide you in the analysis, including the paper produced by the tool authors. https://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise And see: http://cufflinks.cbcb.umd.edu/howitworks.html#hdif In short, fold change is the log2 ratio of FPKMs between the two inputs (not simply just a FPKM). If 0, then there is no change; if 1, a 2-fold change, etc. There are also many resources online in general and specific to expression analysis that explain this in more detail. Even if these focus on microarray data, many of the underlying concepts will apply broadly to most (all?) expression analysis, regardless of the technique to obtain the primary data. Good luck, Jen Galaxy team On 11/29/12 10:10 AM, Ianiri, Giuseppe wrote: Thank you Jennifer. I just start working with these things, so I am wondering which minimal value of FPKM I should use in the filter tool. Do you have an advice or an example that I could look at? Thank you Giuseppe Ianiri, Ph.D. Division of Cell Biology and Biophysics *From:* Jennifer Jackson [j...@bx.psu.edu] *Sent:* Thursday, November 29, 2012 10:51 AM *To:* Ianiri, Giuseppe *Cc:* galaxy-user@lists.bx.psu.edu *Subject:* Re: [galaxy-user] filter for +/- 2-fold difference in expression levels Hello Giuseppe, Fold is included in the Cuffdiff output. Section Differential expression tests, first file, column #9. http://cufflinks.cbcb.umd.edu/manual.html A tool like Filter and Sort - Filter could be used to subset specific values. Hopefully this helps, Jen Galaxy team On 11/29/12 5:35 AM, Ianiri, Giuseppe wrote: Hey guys, I have my Cuffdiff output and I was trying to figure out how to get the data I need. I am interested in the outputs Transcript and Gene differential expressed. Does anyone know how to filter for +/- 2-fold difference in expression levels? Thank you Giuseppe Ianiri, Ph.D. Division of Cell Biology and Biophysics School of Biological Sciences 5100 Rockhill Road University of Missouri-Kansas City Kansas City, MO 64110 Email: iani...@umkc.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/ -- Jennifer Jackson http://galaxyproject.org -- 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] How good is Galaxy as a data repository and for cross-experiment querying?
I'm looking for a tool to manage all of our experimental data, not only the workflow but the storage and meta-analysis as well. I know Galaxy is known for workflow management, but I wasn't sure if it can be used as a cross-experiment repository and querying tool. An example of the query we want to do is for a given gene, find out which cell lines/tissues it's been expressed in all of our RNA-seq and microarray experiments. Does Galaxy have this feature or should I look elsewhere? Thanks. Yuhao ___ 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] Cuffdiff without gene annotation
Hello guys, I went through the RNAseq workflow (I didn't do Cuffmerge) and from the Cuffdiff output gene and transcript differential expression testing I filtered some data. For example, for two samples I got about 400 gene and 900 transcript differential expressed with fold change 2. Since I am working with a fungus whose genome annotation is in a format (gff) not accepted by Cuffmerge or Cuffcompare in Galaxy (the accepted one is GTF2), the Cuffdiff output tells me only the position of relevant genes on the scaffolds. Going to genome browser and see which gene is in that position is fine for few genes, but doing that for all 400 or 900 is something probably impossible. Does anybody have a helpful suggestion on what I can do? It would be great if there was a program where based on the position of the genes on the scaffold (Cuffdiff output) I can get their information using the annotation file. I have also the gene annotation file in gene bank format (gbk) but I don't see a way to use it for what I need. Thanks Giuseppe Ianiri, Ph.D. Division of Cell Biology and Biophysics School of Biological Sciences 5100 Rockhill Road University of Missouri-Kansas City Kansas City, MO 64110 Email: iani...@umkc.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] User's information
Where are the user's information stored in Galaxy? I can't find the information in universe_wsgi. Regards, Sachit ___ 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/
