July 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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queue rules for multi-step workflows
by zuzmus 03 Oct '13

03 Oct '13

Dear Galaxy managers, I would like to ask about the queuing rules for the workflows before processed on the server? I use my customized Galaxy workflow which contains 22 following steps (basically, filtering, trimming and format change of NGS data). I guess the server is generally very busy during last weeks/months (?), so my job was waiting about 24 hours in a queue (which would not be a problem), and then the first step of the workflow was processed, but the following 21 is again/still waiting (already for another couple of hours...). It makes me wondering about the queuing rules because I expected that the whole workflow is queued as one job.. Then my question is if the whole workflow, once submitted, is listed in the queue, or does the following step queue only after the previous step is finished (which would mean to wait the whole queue for each step of the workflow...)? I routinely used those wrokflows before (months ago) without any problems... I tried to search similar question in the archive before I posted this one... Thanks a lot for your answer, My best Zuzana Musilova -- Zuzana Musilova, PhD. (zuzmus(a)gmail.com) Zoological Institute University of Basel Vesalgasse 1, CH-4051 Basel Switzerland - Europe

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Connecting to new Galaxy Cloudman by FTP
by Mohammad Heydarian 27 Aug '13

27 Aug '13

Hi, I am having trouble setting up a FTP connection with the recently released version of Galaxy Cloudman (ami-118bfc78). I have instantiated the new version of Galaxy Cloudman with CloudLaunch<http://usegalaxy.org/cloudlaunch> and also through the AWS EC2 wizard (using the same security group settings as the previous versions) and neither instance will connect to my FTP connection. Has anyone else had this problem? Does anyone know what is preventing the FTP connection? Any help would be greatly appreciated. Cheers, Mo Heydarian

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FTP problem
by Karen Schwarzberg 07 Aug '13

07 Aug '13

Hello, I am using the Galaxy server and I am trying to upload files. I do not see the FTP option even when logged in. Please advise. Best regards, Karen

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rattus norvegicus reference genome
by Matthew Girgenti 06 Aug '13

06 Aug '13

Hi I'm currently using the Galaxy pipeline to analyze my illumina chip-seq data. When I try to use "NGA: Mapping>Map with Bowtie for Illumina" to map my reads there is no rat reference genome. I says I should contact galaxy. Should I simply upload the genome to proceed with analysis? Thanks Matt

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Problem with ftp connexion to Galaxy
by Fabrice BESNARD 06 Aug '13

06 Aug '13

Hello, I registered some time ago to Galaxy. >From the very beginning, my ftp connexion is not working. I am using Filezilla, on a windows operating system. More precisely, the connexion can be established, but the process fail when it is asking for the password. Statut : Résolution de l'adresse de main.g2.bx.psu.edu Statut : Connexion à 128.118.250.4:21... Statut : Connexion établie, attente du message d'accueil... Réponse : 220 ProFTPD 1.3.4b Server (Galaxy Main Server FTP) [::ffff:128.118.250.4] Commande : USER fbesnard(a)biologie.ens.fr Réponse : 331 Password required for fbesnard(a)biologie.ens.fr Commande : PASS *************** Réponse : 530 Login incorrect. Erreur : Erreur critique Erreur : Impossible d'établir une connexion au serveur I sent an email two month ago to report this problem. I was answered that this was an issue happening with the new accounts created. Obviously, this issue has not been fixed yet, has it? If yes, could you indicate me to make my ftp connexion works now ? Thank you for your help !! -- Fabrice Besnard Institute of Biology of the Ecole Normale Supérieure (IBENS) 46 rue d'Ulm, 75230 Paris cedex 05, France 8th floor. Office: Room 802. Lab: Room 817. mail: fbesnard(a)biologie.ens.fr Tel: +33-1-44-32-39-44

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Problem with downloading
by GANDRILLON OLIVIER 06 Aug '13

06 Aug '13

Hi I am trying to download the results of my analysis (.sam files) from Galaxy main. The download gets interrupted about halfway, with no error message, as if the full file had been downloaded (but has not). Thank's for your help Best Olivier Gandrillon

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SNPeff
by Andréanne Morin 06 Aug '13

06 Aug '13

Hello, I would like to use SNPeff for annotation through GATK, However when I upload my file it seems like I cannot use it for this task. My file is .txt and is in this format : Chr location ref allele alt allele 1 1234567 A T/C What am I doing wrong? Thanks, Andréanne

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Filter fastq by percentage of ambiguous (N) bases
by Anto Praveen Rajkumar Rajamani 06 Aug '13

06 Aug '13

Hello, I like to filter my fastq files (50 bp single end Illumina RNA seq reads) by a maximum threshold (10%) of ambiguous (N) bases. I can see that the "CLIP" tool removes all reads with one or more N bases. Is there a way to remove only the reads with five or more N bases using Galaxy? Thank you. Best wishes, Anto

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