December 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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Sort sam or bam
by Clare Sloggett 23 Jan '12

23 Jan '12

Hi galaxy users, Am I right in thinking there is no tool for sorting a sam/bam file in Galaxy? I think this has probably been discussed before, sorry. I just want to check I haven't missed anything, since sibling tools from e.g. the samtools and picard suites are wrapped. Thanks, Clare -- E: sloc(a)unimelb.edu.au P: 03 903 53357 M: 0414 854 759

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Looking for an easy "load test" for Galaxy Cloudman
by Greg Edwards 22 Jan '12

22 Jan '12

Hi, I'm experimenting with Galaxy Cloudman, and could use a simple workflow to a) test that Galaxy is working ok b) put some significant load on a Galaxy server so that it shows in the load diagram, ie. as below [image: load.png] Suggestions appreciated. Thanks, -- Greg Edwards gedwards2(a)gmail.com

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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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Galaxy Bowtie alignment stats report
by Eric Guo 18 Jan '12

18 Jan '12

Hello, Does anyone know how to get alignment stats from Bowtie on Galaxy? I would like to know what percentage of total reads from my dataset is aligned. I know if you run Bowtie using the command line, it gives you the report. However, I could not find percent alignment on Galaxy. Thanks in advance for the help! -Eric

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