- galaxy-user - lists.galaxyproject.org

What's the PV of Galaxy
by liubiao 17 Sep '13

17 Sep '13

Hello Nabble, I am interested the Galaxy and want to set up a local galaxy. Could you address me the PV of galaxy one day? Best Regard, Biao Liu System Engineer Email: liubiao(a)genomics.cn | M. +86 186 7677 1486 China National GeneBank http://nationalgenebank.org/en/index.html Building No.11 | Beishan Industrial Zone | Yantian | Shenzhen China

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MACS on galaxy not responding
by Amit Pande 17 Sep '13

17 Sep '13

Dear Galaxy, I have been trying to run MACS since the past two days but in vain. Could you kindly inform about the problem. My user account : genebuster(a)googlemail.com warm regards, Amit.

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Re: [galaxy-user] FTP Error 530 Sorry, the maximum number of clients (3) for this user are already connected.
by Sobrera, Edwin 17 Sep '13

17 Sep '13

Hello, I too have been repeatedly receving the FTP error as reads in the subject line of the email when trying to connect. I've done everything possible to end all connections, and still get this error. Could you advise if there is any other step that I can take to reset connections? I had a file upload going, but it ended about half-way through and notified me to re-try login. I did try the log on again, and ended up receiving the FTP error message and have been unable to connect since (3 days ago). Thanks, Ross --------------------------------------------------------------------- CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or legally privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of this original message. ---------------------------------------------------------------------

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problem with cuffdiff
by Ianiri, Giuseppe 16 Sep '13

16 Sep '13

Hy guys, I am performing some RNA sequencing. I am using a gtf file as a reference annotation for the cufflink - cuffmerge steps. Then when I do the cuffdiff I find something strange. Where there is the gene name, the corresponding values (all of them!) are 0, where there is no gene name there are values of expression, fold change etc. Does anyone have an idea of what is going on? I haven't find any similar question in the Galaxy archive. Also, I tried to visualize my outputs (TopHat Cufflink Cuffmerge) using Trackster but it gives me an error. Is anyone experiencing the same problem? Thanks, Giuseppe

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Unable to visualize the Tophat accepted hits by Trackster tool
by Zhu Pinkuan 16 Sep '13

16 Sep '13

Hello, My name is Pinkuan, and I have been analyzing some RNA-seq data these days, but I confronted a problem when I did the visualization of the Tophat recepted hits with the Trackster tool. When I add the data of Tophat recepted hits to the visualization tool, there turns out to be an error that I can not visualize the data. So, do you have any idea about how to solve this problem? Greatly thanks, Pinkuan

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CloudMap
by Isaac Knoflicek 16 Sep '13

16 Sep '13

Has anyone out there gotten CloudMap to work in on a local Galaxy instance? https://main.g2.bx.psu.edu/cloudmap I believe I have all the prerequisites installed but when I try to import any of the published workflows I get a "TypeError: expected string or buffer". Any advice would be greatly appreciated. Thanks, Isaac Knoflicek IT Manager - Laboratory of Genetics University of Wisconsin - Madison

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display at ucsc error
by lilach noy 12 Sep '13

12 Sep '13

Hey there, I am trying to add a custom track of a bed file through Galaxy and i keep getting this error: - Error line 325149 of https://main.g2.bx.psu.edu/root/display_as?id=11632524&display_app=ucsc&aut…: chrM_rCRS not a recognized sequence (note: sequence names are case sensitive) it happens Whether i try to upload the file as a track directly or if i do via Galaxy options. Any one knows anything about this issues? Thanks!

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extension of read length
by Tobias Hohenauer 11 Sep '13

11 Sep '13

Dear all, I am working on an MNAse-Seq experiment with 50bp single end reads. To identify nucleosome positions, I read that one needs to extend the single reads to approximately the length of nucleosome protected DNA, being approximately 150bp. Is there a way in Galaxy to extend 50bp reads to 150bp length, lets say from a .BAM file with mapped reads? Of course any other comment on this topic is much appreciated! Thank you very much, Tobias -- Tobias Hohenauer, PhD GCNA, Disease Mechanism Research Core RIKEN Brain Science Institute 2-1 Hirosawa, Wako-shi 351-0198 Japan

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(no subject)
by Maria Hoffman 11 Sep '13

11 Sep '13

Hello, I am fairly new to galaxy and I am trying to use bowtie2 to map my reads against a custom genome (specifically a ribosomal RNA fasta file). I have formatted the file as suggested in the Galaxywiki ect and I am still getting the following message: Job output not returned by PBS: the output datasets were deleted while the job was running, the job was manually dequeued or there was a cluster error. Any help would me much appreciated! Maria

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Data sources don't load in Firefox
by Ganote, Carrie L 11 Sep '13

11 Sep '13

Hi List, I'm trying to go through Galaxy 101, and the first step is halting me (UCSC Main table browser does nothing on click). I'm giving a presentation on how to use Galaxy, but the data sources do not load when using Firefox. The tool click registers, because the history pane is minimized, but the URL is not invoked (no activity from browser). I went through my FF settings to see if I'm doing anything to block iframe loads. The funny thing is, though UCSC and BX don't load, but Biomart does - likely because it is not in an iframe but gets loaded as its own window. If I open in a new tab, it's fine. These things load on Chrome, IE and Safari. A lot of my users use Firefox, however. I appreciate any insight into this. Sincerely, Carrie Ganote

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