November 2012 - galaxy-user - lists.galaxyproject.org

"Metadata is being auto-detected" stuck in continuous loop
by Redvers Richard 30 Nov '12

30 Nov '12

Greetings, Recently on the Main Galaxy site, on numerous occasions, when trying to convert a tabular dataset datatype to an interval format, Galaxy attempts to detect Metadata - but continues unabated in this loop for days on end, both with Biomart datasets and my personal custom datasets, with no end in sight. Copying the dataset to a new history seems to fix this, but surely there must be a better workaround than constantly shuffling things into new histories when converting to interval format? Any advice would be greatly appreciated. Regards, Rick Richard P. Redvers, PhD Metastasis Research Laboratory Cancer Cell Biology Program Peter MacCallum Cancer Centre p: +61-3-9656-3713 (Office) +61-3-9656-1285 (Lab) f: +61-3-9656-1114 w: http://www.petermac-research.org/ Mailing Address: Courier Address: Locked Bag #1 2 St Andrew's Place A'Beckett St East Melbourne East Melbourne Victoria, 3002 Victoria, 8006 AUSTRALIA This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.

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Cuffdiff without gene annotation
by Ianiri, Giuseppe 30 Nov '12

30 Nov '12

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: ianirig(a)umkc.edu

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filter for +/- 2-fold difference in expression levels
by Ianiri, Giuseppe 30 Nov '12

30 Nov '12

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: ianirig(a)umkc.edu

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How good is Galaxy as a data repository and for cross-experiment querying?
by Yuhao 30 Nov '12

30 Nov '12

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

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trim adapters and other
by Zhiqiang Shu 30 Nov '12

30 Nov '12

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

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Clip doesn't see my FASTQ file
by Stephen Eacker 30 Nov '12

30 Nov '12

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 seacker1(a)jhmi.edu

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Stitch Gene blocks return empty result???
by 张坤山 30 Nov '12

30 Nov '12

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_00007949 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_00007949 >hg19.TCONS_00007949 >panTro2.TCONS_00007949 No sequence in result.What happen?? Kunshan

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Data/history/user export and import
by Bossers, Alex 30 Nov '12

30 Nov '12

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

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Bismark Error: Data table named 'bismark_bs_indeces' is required by tool but not configured.
by Sachit Adhikari 29 Nov '12

29 Nov '12

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

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combining two fastq files
by shamsher jagat 28 Nov '12

28 Nov '12

Is there an option in galaxy to combine two fastq files? Thanks kanwar

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