May 2013 - galaxy-user - lists.galaxyproject.org

Help with Summary Statistics
by D. A. Cowart 23 May '14

23 May '14

Hello, I am attempting to use Galaxy to calculate the mean sequence read length and identify the range of read lengths for my 454 data. The data has already been organized and sorted by species. The format of the data is as follows: >HD4AU5D01BHBCQCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC >HD4AU5D01A093MCTCTGTCGCTCTGTCTCTCTTCTCTCTCTCTCTCTCT etc...for each species I have attempted to use the "Summary Statistics" button, however it appears to only be for numerical data and not sequence data. Is this tool/task available via Galaxy? Thank you, Dominique Cowart User name: dac330

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SNP finding
by Xiefan Fang 03 Dec '13

03 Dec '13

Dear galaxy users, We have done deep sequencing on some known genomic loci using Hiseq2000. I have already mapped the reads to the reference sequences by using Galaxy. In the next step, I want to find SNPs and calculate the SNP percentage within the reads. There are 500,000 to 1,000,000 reads per biological sample. Can I do it with galaxy? If not, is there other programs available in windows? Considering that I am not very familiar with programming. Thanks, Xiefan University of Florida

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analysing pooled data with FreeBayes
by Nicola Smith 24 Jul '13

24 Jul '13

Hi, I am new to this and I hope someone can help. I have pooled sequencing data that I am trying to analyse using Galaxy. I've done quite a bit of online searching and it seems that FreeBayes should be able to do this, if I select "set population", click the "Assume that samples result from pooled sequencing" option and change the ploidy to nx2 (number of alleles, where n is the number of subjects and the organism is diploid). However, whenever I do this I get an error: usually just "Killed" I was originally setting my polidy rather high (190 as I have 95 subjects pooled), so I wondered if this was the problem, however, it fails if I do a ploidy of only 4 too. I've tried various things to try to see where I am going wrong: All with the same BAM file: Set population model options: Do not set --> works Set population model options: set, Assume that samples result from pooled sequencing: not ticked, Default ploidy for the analysis: 2 --> works Set population model options: set, Assume that samples result from pooled sequencing: ticked, Default ploidy for the analysis: 2 --> works Set population model options: set, Assume that samples result from pooled sequencing: ticked, Default ploidy for the analysis: 4 --> fails (killed) Set population model options: set, Assume that samples result from pooled sequencing: ticked, Default ploidy for the analysis: 10 --> fails (killed) Set population model options: set, Assume that samples result from pooled sequencing: ticked, Default ploidy for the analysis: 10 --> fails (killed) It seems that it is the ploidy part that I am doing wrong, as it works with pooled data but ploidy of 2. I'm sure I have to change the ploidy though, or else how does the program know how many subjects are in the pool? Also, everywhere that I've ready says you have to change the ploidy. I apologise if my question is naive. As I said, I am new to Galaxy and this is the first thing I am trying to do! Any help / suggestions would be appreciated, Thanks, Nic

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barcode splitter files web based
by Ann Holtz-Morris, M.S. 11 Jul '13

11 Jul '13

HI, I'm trying to use the output files from barcode splitter. I know that the command line as some wrappers made that take the output files and puts them in the history. Is there anything similar for output files but for us biologists who don't do command line? J Thanks, Ann CONFIDENTIALITY NOTICE: This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you.

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Newbie: summary or metrics of Galaxy use & adoption?
by Ramon Felciano 03 Jun '13

03 Jun '13

Hello all - I would like to evaluate Galaxy for integration with Ingenuity's NGS analytics platform, and am trying to pull together some macro materials on how Galaxy has been used and adopted by the community at large. Are there any presentations or wiki pages that summarize basic stuff like: # users # of deployments/ instances (public or private) Relative use of CloudMan vs locally deployed Use in any clinical or regulated environments (e.g. CLIA) I've seen the materials at http://wiki.galaxyproject.org/Galaxy%20Project/Statistics but this looks to be only related to the public instance. Are there any similar materials that summarize across all installations, perhaps based on user surveys or the like? Thanks in advance for your help. Ramon ____________________________________ Ramon M. Felciano, PhD Founder and SVP, Research INGENUITY Systems, Inc. 1700 Seaport Blvd., 3rd Floor Redwood City, CA 94063 650.381.5100 phone 650.963.3399 fax E-mail: felciano(a)ingenuity.com<mailto:felciano@ingenuity.com>

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Information for Galaxy Event Horizon
by Sarah Maman 03 Jun '13

03 Jun '13

Dear all, Four days of training in genomics are occurring on our local instance of Galaxy (27-30 May). This training session takes place at INRA, Toulouse Auzeville, France, as part of a collaboration between Sigenae (http://www.sigenae.org/) and GenoToul bioinformatics platform (http://bioinfo.genotoul.fr/) This session is composed of four training days: * Galaxy first step * Reads alignment and SNP calling * RNAseq alignment and transcripts assemblies * sRNAseq Do you think it is possible to list our training session in your "Galaxy Event Horizon"? Sincerely, Sarah Maman -- --*-- Sarah Maman INRA - LGC - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 --*--

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List of genomes
by YBao 01 Jun '13

01 Jun '13

Hi All, I was trying to map a set of data to a genome, Klebsiella pneumoniae subsp. Pneumoniae MGH 78578(31). While uploading the reads, I was able to find the reference genome as listed above. However, when I tried to map the data using wither bowtie or BWA, the pull down list did not include this genome. Can someone help or enlighten me as why it did not make into the list? Thanks Yongde -- Yongde Bao DNA Sciences Core Dept. of Microbiology, Immunology, and Cancer Biology UVA

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uploading files to main galaxy at psu
by Colaneri, Alejandro Cesar 31 May '13

31 May '13

I'm trying to upload fastq files to the server. I have 52 fastq files, Two days ago I started with 8 of them. Two files were upload in the first hs, however after more than 48 hs the rest of the files are still trying to be uploaded. It is this normal? Dr. Alejandro Colaneri Departments of Biology University of North Carolina at Chapel Hill 310 Coker Hall, CB# 3280 120 South Road Chapel Hill, NC 27599-3280 Tel: 919-962-2273 fax: 919- 962-1625

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June 2013 Galaxy Update
by Dave Clements 31 May '13

31 May '13

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Re: [galaxy-user] tophat to cuffdiff without cufflinks
by Colaneri, Alejandro Cesar 31 May '13

31 May '13

Well in that case I will like to use the same gtf file from TAIR 10 that was used by the tophat. But the tophat have the option bult in. How can I point cuffdiff to the same file? Dr. Alejandro Colaneri Departments of Biology University of North Carolina at Chapel Hill 310 Coker Hall, CB# 3280 120 South Road Chapel Hill, NC 27599-3280 Tel: 919-962-2273 fax: 919- 962-1625 From: Jennifer Jackson <jen(a)bx.psu.edu<mailto:jen@bx.psu.edu>> Date: Thursday, May 30, 2013 8:07 PM To: "Colaneri, Alejandro Cesar" <colaneri(a)email.unc.edu<mailto:colaneri@email.unc.edu>> Cc: "galaxy-user(a)bx.psu.edu<mailto:galaxy-user@bx.psu.edu>" <galaxy-user(a)bx.psu.edu<mailto:galaxy-user@bx.psu.edu>> Subject: Re: [galaxy-user] tophat to cuffdiff without cufflinks Hello, You will need to provide a GTF or GFF3 file to Cuffdiff - this is what the tool uses as a reference base to build gene, transcript, and if provided in the annotation attributes, transcript start site and protein groupings to perform the differential analysis. More details can be found here: http://cufflinks.cbcb.umd.edu/manual.html Our tutorial and other wiki help is linked from here, see "Tools on the Main Server": http://wiki.galaxyproject.org/Support#Interpreting_scientific_results Hopefully this helps, Jen Galaxy team On 5/30/13 3:15 PM, Colaneri, Alejandro Cesar wrote: Hi I comparing gen expression data (RNA-seq) in Arabidopsis. Different genotypes, different conditions. Since Arabidopsis is very well annotated I decided to do cuffdiff directly after tophat. However when building my workflow I found that the cuffdiff said a gtf file is necessary. Please see the picture in this email, under INPUT FORMAT. My question is if I can still compare my libraries in the way I designed below. [cid:part1.04070709.03020802@bx.psu.edu] Dr. Alejandro Colaneri Departments of Biology University of North Carolina at Chapel Hill 310 Coker Hall, CB# 3280 120 South Road Chapel Hill, NC 27599-3280 Tel: 919-962-2273 fax: 919- 962-1625 ___________________________________________________________ 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 Galaxy Support and Training http://galaxyproject.org

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