- galaxy-user - lists.galaxyproject.org

Problem with repeated genes in Cuffdiff's output
by Hoang, Thanh 17 Jul '13

17 Jul '13

Hi all, I am working on RNA-seq using TopHat/Cufflink/Cuffdiff for differential gene expression and new gene discovery ( this is what I am interested in). However, I found many genes that are repeated in the Cuffdiff's ouput. These are the same genes and at the exact the same locus. There should be only one gene for 1 line. Something like this: *Genes* *Locus* *Status* *q1* *q2* *Log2 Folg change* *Significance* * Lnp* *2:74517521-74584544* *OK* *8.91501* *85.2735* *3.25779* * yes* *Lnp * *2:74517521-74584544* *OK* *12.0044* *171.352* *3.83533* * yes* If I re-run the Cuffdiff for differential gene expression only ( No gene discovery), the problem is fixed. Anyone knows how o explain and fix this? Thank you so much

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Emptying my account for good
by GANDRILLON OLIVIER 16 Jul '13

16 Jul '13

Hi I am trying to get rid of all my previous files, in order to upload new ones. I usually use "delete permanently" for that, but this time, only used "delete". And now I am stuck: the site says I am using 69 % of my account, although my history is empty, and everything is empty, and 100 % should be available for new analysis... I tried the "purge deleted datasets" but to no avail. Thank's for your help Best Olivier Gandrillon

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Error running Metagenomic Analysis
by Pavan Kumar 15 Jul '13

15 Jul '13

Hello, I am have created the workflow for metagenomic analysis. I am using fetch taxonomic representation tool. But it is showing me the error like "*ERROR in line 1: Invalid ID tag" *irrespective of the data. There are few questions raised about the same error in the blog, but the solution is not conviencing. Please help me in troubleshooting the above error Thanks in advance -- Pavan

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Evaluating TopHat's results
by Hoang, Thanh 15 Jul '13

15 Jul '13

Hi, I ran TopHat on Galaxy for my RNA-seq data. I want to analyze TopHat's output files, such as percentage of reads mapped to the genome...but I am not sure how to do that. I am also trying to visualize the BAM file by IGB but the following error message appears : " Failed to authenticate to the server". Anyone can help with these issues? Thank so much Thanh

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Extreme Newbie Question
by Seth Stern 15 Jul '13

15 Jul '13

Hi Everyone, I recently uploaded about 1.8 GB of MiSeq reads (using ftp). The upload seemed to go fine, but Galaxy seems to be very unhappy with the file. I'm seeing the following message in History: 1: miseq_R1-03-07-2013.zip empty format: txt, database: <https://main.g2.bx.psu.edu/datasets/bbd44e69cb8906b504f52516868a1f84/edit> ? ZIP file contained more than one file, only the first file was added to Galaxy. Can anyone tell me how to diagnose the problem ? Many thanks, Seth Seth Stern, Ph.D. sethster(a)comcast.net 650 996 8726 (cell)

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bugs of snpSiftWrapper.pl corrected
by Yufei LUO 15 Jul '13

15 Jul '13

Hi, For those who use snpEff V3_3c release in Galaxy. There are two little bugs in snpSiftWrapper.pl. You can find the corrected file in the attachment. Best Regards, -- Yufei LUO Bioinformatician Insitut Gustave Roussy Bâtiment de Médecine Moléculaire Bureau N°136 114, rue Edouard Vaillant 94805 Villejuif Cedex - France

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galaxy online difficulty?
by Elizabeth Clare 15 Jul '13

15 Jul '13

Hi, I've been using galaxy (online) for over a year now without too many issues. Over the last week I can't seem to get anything done. Tasks that normally take seconds are taking overnight and have now stopped entirely. I can't see anything in the twitter feed or news about server maintenance. The types of tools I'm using are simple "reverse compliment" or "barcode splitter" and the data sets are small (some are only a few hundred reads). So these should be very quick tasks. Is there a way I can test whether the problem is at my end? Thanks! fantastic analysis package! Elizabeth -- -------------------------------- Dr. Elizabeth L. Clare School of Biological and Chemical Sciences Queen Mary University of London Mile End Road, London E1 4NS Room 1.02, G. E. Fogg Building e.clare(a)qmul.ac.uk +44 (0)207 882 5687 http://webspace.qmul.ac.uk/eclare/ "If you say yes more often than you say no, you will do interesting things in your life"

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command under the hood
by Kaiyin Zhong (Victor Chung) 14 Jul '13

14 Jul '13

Hi, dear list. We are right now using Galaxy for the pileup of some of our BAM files, but we also would like to be able to use samtools to generating the same results on our own PC. The options we use on the web interface are the simplest, as shown in this screenshot: http://imgur.com/WCwVBvG Can anyone inform us what are the commands and options under the hood? Thanks! Best regards, Kaiyin ZHONG ------------------------------ Forensic Molecular Biology, Erasmus MC k.zhong(a)erasmusmc.nl kindlychung(a)gmail.com

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downloading problems from main Galaxy
by Elwood Linney 11 Jul '13

11 Jul '13

Problem: > when downloading steps in histories back to my computer the files are sometimes incomplete (by incomplete I mean a significantly smaller size that given during the download indicator) Description: >after processing RNAseq files on main Galaxy I have the memory to download steps or complete histories; this past week I have noticed, in a random way that some individual tophat alignments or cuffdiff analyses do not download completely to my computer--sometimes they do, but its random right now Questions: Is there something I can do to eliminate this? Does this have anything to do with how busy Galaxy is? I notice that it sometimes happens even if I try to download one file at a time el linney Duke University Medical Center

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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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