November 2012 - 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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extracting a subset of sequences from a very large fasta file(1.5 million)
by Perumal Vijayan 15 Feb '13

15 Feb '13

I have successfully uploaded a large fasta file (2.5 million genomic sequence contigs) onto Galaxy server. I wish to extract a subset of sequences from this file. I have a list of the fasta headers. Is there a way I can accomplish this on Galaxy? -- Perumal Vijayan Saskatoon Canada

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Re: [galaxy-user] Batch jobs...
by Neil.Burdett＠csiro.au 04 Jan '13

04 Jan '13

Do i need to modify a setting in universe_wsgi.ini or somewhere then ? As I attach screenshots of what I've got (I have a recent subversion checkout)... Thanks Neil [cid:image001.jpg@01CDB754.FC6C6330] [cid:image002.jpg@01CDB754.FC6C6330]

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dataset not visible
by Ilse Vandecandelaere 01 Dec '12

01 Dec '12

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/ -----------------------------------------------------------------

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History Pane empty?
by jason gagliano 01 Dec '12

01 Dec '12

Hi I just had a quick question. My History pane to the right of my Galaxy account on the web suddenly was empty when I logged in. I noticed that I can still find all my datasets under "Saved History" or "Saved Datasets" but nothing will show up now in the history pane. This is true even when I upload a new data set. Any thoughts on the problem and a solution? Thanks Jason P.S. I have read all I could find on the topic in the help sections before asking this question. But I could not find anything that worked for me (like simply deleting cookies). I am relating this to say that I am trying to be a good citizen by reading first and then asking questions :0)

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Re: [galaxy-user] Analysis in queue but not running
by Dave Clements 30 Nov '12

30 Nov '12

Hi Lew, CC'ing the galaxy-user list because I am assuming that your question is about the free public server ("Main") @ usegalaxy.org / main.g2.bx.psu.edu. If you have any future questions about Main, please post them to Galaxy-User so that others can see the question and respond. If I am reading the qstat output correctly, there are currently ~140+ jobs in the NGS queue, which means that Main is currently under very heavy load. The best thing to do is let the jobs sit in the queue. Killing and restarting them bumps them to the end of the queue. We are currently discussing a number of options for letting users know in situations like this, that while the job is not currently running, it is in the queue, and is moving forward. Thanks, Dave C PS: and the number of jobs in the queue has dropped by 2 since I started typing this email. On Fri, Nov 30, 2012 at 10:05 AM, Lewis Bowman <lbowman(a)mailbox.sc.edu>wrote: > I have tried repeatedly to run Cuffdiff using cuffmerge output (38) and > cufflinks output (25 and 29). In every case the job does not begin to run > and status says"Job is waiting to run." Has Galaxy been down for the last > several days? I am unsure what to do since I have received no error > message. Thanks for you help. > > Lew Bowman > > -- > Lewis H. Bowman > Department of Biological Sciences > University of South Carolina > Columbia, SC 29208 > PH: 803-777-5157 > FAX: 803-777-4002 > EMAIL: lbowman(a)mailbox.sc.edu > > -- <http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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December 2012 Galaxy Update
by Dave Clements 30 Nov '12

30 Nov '12

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Cuffdiff tracking file does not report all genes and trancrips from reference annotation?
by Wei Liao 30 Nov '12

30 Nov '12

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

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User's information
by Sachit Adhikari 30 Nov '12

30 Nov '12

Where are the user's information stored in Galaxy? I can't find the information in universe_wsgi. Regards, Sachit

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