November 2011 - galaxy-user - lists.galaxyproject.org

question about uploading data through URL method
by Xiangming Ding 20 Mar '12

20 Mar '12

Hi galaxy I am a new user of galaxy. i met a problem and didnot find similar question in FAQ. I wanted to upload the data from DDBJ DRA dataset to galaxy through UTL method. The file is around 800M. However after uploading, the FASTQ file was just around 2M. So I wanted know whether it is possible to upload a large file to galaxy through URL method? or I should download the file to my pc and then uploading to galaxy through FTP method. Thanks xiangmimg

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New Genome Load Request
by Mark Guiltinan 26 Jan '12

26 Jan '12

Hello Galaxy, Would you please perform the following new genome load? Theobroma cacao All the necessary resource files can be found and downloaded at: http://cocoagendb.cirad.fr/gbrowse/download.html Thank you Mark Guiltinan Mark Guiltinan Professor of Plant Molecular Biology Penn State University Department of Horticulture 422 Life Sciences Building University Park, PA 16802-5807 Phone 814 863-7957 mjg9(a)psu.edu Web Site: http://guiltinanlab.cas.psu.edu

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fetch sequence functionality
by Lawrence Mckechnie 19 Jan '12

19 Jan '12

Hi, I uploaded a tab-delimited file(this was constructed within R using write.table) into Galaxy with chr, start, end, and esembl_TSS_name. Whilst I am able to use fetch sequence function, currently not able to include the Esembl ID in the FASTA output. I am able to include the Ensembl name in the interval format but not in FASTA format. thanks, Lawrence

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FASTQ joiner
by Matthew Herron 19 Jan '12

19 Jan '12

I am trying to join two groomed fastq files from a paired-end Illumina read using the fastq joiner tool. The drop-down menus correctly identify the groomed fastq files, but after cranking for a few minutes the tool produces empty output: "FASTQ joiner on data 5 and data 4 empty format: fastqsanger, database: ? Info: There were 3497909 known sequence reads not utilized. Joined 0 of 3497909 read pairs (0.00%)." The files have the same number of reads (3497909), reads have the same number of bases (102), and the joiner tool doesn't have any options (other than choosing the two files to join). Can anyone tell me what I'm doing wrong? Thanks, -- Matthew D. Herron, PhD Department of Zoology University of British Columbia X.princeps(a)gmail.com http://www.eebweb.arizona.edu/grads/mherron/

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Operate on genomic intervals: Join
by Stephen Eacker 19 Jan '12

19 Jan '12

Hello, I using operate on genomic intervals on some data and it always seems to ignore the strand information. Am I missing something or does "operate of genomic intervals" disregard strand information? Is there a tool that does the inner join function and takes into account strand information? thanks, Steve Stephen Eacker, Ph.D. Postdoctoral Fellow Dawson Lab Institute for Cell Engineering Johns Hopkins Medical Institute (443) 287-5605 seacker1(a)jhmi.edu

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cufflinks FPKM
by Li, Jilong (MU-Student) 19 Jan '12

19 Jan '12

Hi, I want to use cufflinks handle the results of Tophat. Cufflinks uses FPKM to normalize the expression data. I think FPKM is for pair-end reads. right? My reads are single-end. Is it right if I use FPKM? Thank you very much! Victor

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Deleted history
by Herve Rhinn 19 Jan '12

19 Jan '12

Hi, I have not been using Galaxy for a few months an it seems that a least one of my history was deleted. I assume it is because of inactivity for too long/exceeding the new quotas. Would there be by chance a a way to re-access it temporarily to be able to download some of that data or has it been totally erased? Thanks lot, Herve Rhinn

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enabling regular users to upload large data volumes to a local Galaxy server
by Yury V Bukhman 13 Dec '11

13 Dec '11

Hi, we are running a local Galaxy server, administered by a bioinformatics core group. Our end users increasingly come to us with sets of large NGS files that they can't upload to Galaxy on their own through a web browser. We copy their data to a Galaxy filesystem and upload into data libraries from there using the admin interface. However, the users would prefer to be able get their data onto the server on their own. What's the best solution to that? Should we set up FTP upload? Are there other tricks? Any advice would be appreciated. Thanks. Yury -- Yury V. Bukhman, Ph.D. Associate Scientist, Bioinformatics Group Leader Great Lakes Bioenergy Research Center University of Wisconsin - Madison 445 Henry Mall, Rm. 513 Madison, WI 53706, USA Phone: 608-890-2680 Fax: 608-890-2427 Email: ybukhman(a)glbrc.wisc.edu

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Random Intervals ?
by Vincent Joseph Lynch 07 Dec '11

07 Dec '11

To Whom It May Concern, I am curious if there is a tool within Galaxy to generate a set of random intervals from a particular genome similar to the "Random Intervals" tool within the ENCODE tools? I am using the "Aggregate datapoints" tool to get phastCons conservation scores for peaks from ChIP-Seq data. I would like to compare these scores to a random expectation so would like to be able to use a Random Intervals-like tool to generate a set of random positions to compare to the experimental set. Best, Vinny Vincent J. Lynch, Associate Research Scientist Department of Ecology and Evolutionary Biology & Yale Systems Biology Institute Yale University "There is a grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that whilst this planet has gone on cycling according to the fixed laws of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved." -C. Darwin, 1859

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Chip-seq data
by Giuseppe Petrosino 30 Nov '11

30 Nov '11

Hi, I have illumina ChipSeq data in txt format with this structure: @HWI-EAS225:8:1:1:58#0/1 NAGAGTGCCCGGGTTCAGTTCTCAGCACCCATGTGG +HWI-EAS225:8:1:1:58#0/1 DMSSSSSSUSSTTTUTSSSSSSSSSRQRTTTSSSUS @HWI-EAS225:8:1:1:1803#0/1 NCCATGGGAAGAGCTGGGCAGGCGGGCCGAGCGAAG +HWI-EAS225:8:1:1:1803#0/1 DLSTTSKOUTRRTTSSSTTTTSRPNNTOJOTSSRTB @HWI-EAS225:8:1:1:1547#0/1 NAGGGAAAAGTGGGACTGGCACTTGCCTCTACCAGC +HWI-EAS225:8:1:1:1547#0/1 DLVVVTPTVVVVUVVWVVUVVUWVVVWWWWWWWVVV Can I convert into Fastq format?If so, how can I? Furthermore, after using Map with Bowtie for Illumina, how can I use MACS (Model-based Analysis of ChIP-Seq) if I have two files for IP samples and two files for Control samples? Thank you so much. Giuseppe

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