August 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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from Galaxy to Megan
by Judith van Bleijswijk 10 Oct '12

10 Oct '12

Dear Galaxy users that also use Megan, I hope you can help me combining Galaxy with Megan4. I followed the Galaxy metagenome workflow (author aun1) on shotgun DNA 454 sequences of two samples that I would like to compare. The results are two nice trees and tables with the lowest taxonomic ranks for the two samples. Besides the taxonomy I am also interested in the functions and I would like to use Megan4 (with SEED and KEGG classification) for this purpose. I tried to import a Galaxy file (.tabular) with c1 =high quality segment name and c2-c13 =blasthit results and a Galaxy fasta file with the high quality segment names and sequences. This does not work and I receive the message parsing failed, no reads found. I am interested to know how you solved this issue and which files in the Galaxy metagenome workflow you use to import into Megan4. Or maybe there is other software that you use to compare suits of functional genes in your metagenome datasets? Regards, Judith van Bleijswijk

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FTP upload problem
by Yan He 17 Sep '12

17 Sep '12

Hi everyone, When I tried to upload my files using Filezilla, I got the error message "530 Sorry, the maximum number of clients (3) for this user are already connected." Can anyone give me some suggestions how to solve this problem? I have been stuck here for a whole day. Thanks very much! Yan

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What is the minimum Quality should I set for Filter FASTQ?
by Du, Jianguang 13 Sep '12

13 Sep '12

Dear All, I am analysing RNA-seq datasets for differential splicing events between cell types. Some of my reads contain bed nucleotides, should I run Filter FASTQ to remove these "not so good" reads? If I do need to, what is the "Minimum Quality" should I set for the Filter? Thanks. Jianguang

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interupted running jobs restart
by petr 11 Sep '12

11 Sep '12

We are running galaxy on pbs cluster. In out setting some jobs can take several weeks to finish and it is virtually impossible to wait for suitable moment when server can be restarted or turn down without interrupting running tasks. Is there an option on server setting which will enable jobs which were interrupted because of the server maintenance to run again after the cluster is back on? best regards. Petr

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MACS- Duplicate reads removal
by Yanina Bogliotti 04 Sep '12

04 Sep '12

Hi, Does MACS remove duplicate reads automatically during the peak calling? I'm running controls for all the samples. Thanks for your help, Yanina

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No reference genome listed for NGS: Mapping Map with TMAP for Ion Torrent
by Catherine Dumur 31 Aug '12

31 Aug '12

The "Select a reference genome" popup in the NGS mapping section is empty for TMAP for Ion Torrent tool (version 0.0.19) on the Galaxy Web Portal (I am using Galaxy Test, since I only have Ion Torrent data, and the TMAP tool is only on Galaxy Test). How can I populate it? Thank you very much in advance for any help you can provide! Cathy Catherine I. DUMUR, Ph.D. Associate Professor of the Department of Pathology Director of Molecular Morphology Genomics Associate Director of the Molecular Diagnostics Laboratory Co-Director of the Tissue and Data Acquisition and Analysis Core (TDAAC) Virginia Commonwealth University Phone: (804) 828-9564 Fax: (804) 827-4738 NOTE: The information contained in this message may be privileged and confidential and protected from disclosure. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately by replying to the message and deleting it from your computer. -------------------------------------- VCU Health System http://www.vcuhealth.org

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problem running MACS on Galaxy
by Amit Pande 31 Aug '12

31 Aug '12

Dear galaxy, I am trying to run BAM files for Peak calling using MACS and for the larger files above 2GB I am continuously getting no results. Can you please identify the source of this kind of error. warm regards, Amit

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September 2012 Galaxy Update
by Dave Clements 29 Aug '12

29 Aug '12

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Should I "use raw junction" and "Only look for supplied junctions"
by Du, Jianguang 29 Aug '12

29 Aug '12

Dear All, I have two more questions about settings for Tophat. My aim is to look for the defferential splicing events between cell types. After I checked "Use Own Junctions", three more options came out: 1) "Use Gene Annotation Model" 2) "Use raw Junctions" 3) "Only look for supplied junctions" As instructed by Jen, I checked "Use Gene Annotation Model", and input iGenome mm9 genes.gtf as "Gene Model Annotations". However, I am not sure if I should choose to "Use raw junctions" and "only look for supplied junctions". Please help me set up these two options. Thanks. Jianguang

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