September 2006 - galaxy-user - lists.galaxyproject.org

tools: merge regions of a single query
by Erika 28 Sep '06

28 Sep '06

Hi, I've tried using the "Operate on Genomic Intervals" tool called "Merge regions of a single query" with some puzzling results. So from the example provided with the tool it seems that if regions fail to merge (i.e. they are unique) then they should be returned in the output along with the merged results, correct? I have used 3 different data files, for human hg18, chimp panTro2, and macaque rheMac2, and each of these files has returned an empty output result. However, they have successfully completed the operation (no error messages were returned). Does this indicate that all regions are unique? Does this indicate a problem with the input file? Does this indicate a problem with the tool? I have attached an example file. Thank you for your help, Erika ********************************************************** E.M. Kvikstad Academic Computing Fellow IGDP Genetics Center for Comparative Genomics and Bioinformatics The Pennsylvania State University 208 Mueller Lab University Park, PA 16802 (814) 863-2185 kvik(a)bx.psu.edu

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edit attributes is not saving changes
by Erika 28 Sep '06

28 Sep '06

Hi, I'm trying to use the "edit attributes" function and the server is returning a notice indicating "attributes changed" however the attributes changes are not actually being saved. i am specifying a file as "genomic intervals" and i input the columns indicating chromosome, start, end, strand. it's a simple file with only 10 lines. thanks for the help! ********************************************************** E.M. Kvikstad Academic Computing Fellow IGDP Genetics Center for Comparative Genomics and Bioinformatics The Pennsylvania State University 208 Mueller Lab University Park, PA 16802 (814) 863-2185 kvik(a)bx.psu.edu

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No reaction clicking any tools using internet explorer
by Taschner, P. (HKG) 26 Sep '06

26 Sep '06

Using Internet Explorer 6.0, I was unable to select any of the Galaxy tools, although Javascript has been enabled. Clicking on any tools results in the message Error on page. Galaxy tools seem to work using Firefox, so you might wish to include this information on your wiki page. Best regards, Peter Dr. Peter E.M. Taschner Department of Human Genetics Center for Human and Clinical Genetics Leiden University Medical Center Postal zone: S-4-P P.O. Box 9600 2300 RC Leiden The Netherlands Telephone: +31 71 5269424 Fax: +31 71 5268285 E-mail: P.Taschner(a)lumc.nl Visiting address: Building 2, room R04-005, Einthovenweg 20, Leiden

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critical feedback
by Ross Hardison 26 Sep '06

26 Sep '06

This student was more adventurous. I think he actually could do more of what he tried with more experience (if he wants to get GNF data he should use that table), but there is some good feedback. I do agree with one comment - that we should mask out buttons that don't work on the Table Browser proxy. "My goal is to use Galaxy to retrieve gene expression data from GNF human gene expression atlas from UCSC genome table browser. If possible, I will do a gene co-expression analysis for a group of genes that are annotated as G-protein coupled receptors (GPCRs). The first problem I met was that I could not find a place in UCSC genome table browser to retrieve genes with annotations. I think it is reasonable for a biologist to ask questions like: what are the annotated G-protein-coupled receptors or MAP kinases in the human genome. I went though a number of table schema of UCSC genome table browser, there are no annotation in those tables. The lack of gene- annotations in the UCSC table browser may reflect the scope of UCSC designers and is not related to Galaxy, so I will not further discuss this issue. I went to the GNF atlas official website downloaded annotated probe file, and extracted all the genes annotated as G protein coupled receptors. There are totally 385 such annotated probesets in the public available annotation file (by custom Python code search for annotated as “coupled” and “receptor”). I thought it may be possible to do this operation in Galaxy, but I found in the “Filter, sort, join and compare: Select” tool, there is no combinatorial pattern search. It would be helpful to add a place where people with more expertise can customize their query commands and save them. In another word, if people already know a little about PERL or Python, it may be desirable for them to put a short query in those programming languages. After obtaining the list of GPCRs, I was trying to use Galaxy to retrieve data from UCSC table browser. I clicked on GET DATA à UCSC main à Execute, which brought up a proxy page in the middle panel of Galaxy interface. I found at least three functions on this proxy did not work properly. First, the button of “describe table schema” did not work. Second, when I clicked on “upload list”, an uploading interface appeared in the middle panel. When I clicked “submit” after I specified the file name, the middle panel showed “This is a proxy to the data services provided by the UCSC Genome Browser's Table Browser.”. and no data were received by Galaxy. Third problem was when I specified a file name as output file in the “output file: (leave blank to keep output in browser)”, I could not get the output file anywhere. Clearly there are some “mis-communication” between Galaxy and UCSC browser. It may be useful to “mask” these functions in Galaxy to avoid frustration. What I finally did was to “PASTE LIST” of all the probe names I got and retrieve the data from UCSC browser. The resulted file in Galaxy is the same as what I downloaded directly from UCSC browser website use the same set of 385 probesets names. Totally 405 expression data were extracted from the UCSC table browser. The gene expression data was in the column 16 of the output file. I did “cut columns from a table” then “Remove beginning of a file” and then “convert delimiters to tab”. These operations gave me a file with table delimited expression data of 405 probesets(genes). I found that in the data browsers of Galaxy, the maximum number of columns is 27, above that, there was no straight forward way of finding out how many columns were in the data file. Although there is a statistical tool in the Galaxy, we can only calculate “correlation for numeric COLUMNS”. And there is no way to transpose the data matrix. Therefore, I could not find a way to finish my goal completely in Galaxy. I have learned one important lesson from the experience of using Galaxy: the diversity of GENOMICS data is a great challenge for people working on genomic research and for any software. Clearly, Galaxy is a sequence-analysis centric environment. I am sure Galaxy can do a great job in sequence analysis. However, when we are looking for other type of genomics data, for example, gene expression data from microarrays(or Masspec spectrum of proteome data), Galaxy may not be a suitable tool. For example, microarray data usually comes in a format of M by N matrix of numerical data, with more than 10,000 rows and hundreds of columns. The display of Galaxy history frame is not suitable for the display of such data. The statistical tools and graph data tools in Galaxy are clearly designed for sequence data, because in those tools, we cab only do column-wise statistics/ graphics. The query tools in Galaxy are limited to simple queries, where combinatorial query such as “protein AND receptor” can not be effectively performed. Again, this is not a drawback for Galaxy if our starting point is a set of “gene identifiers” and our goal is “sequence analysis”. Yet, I think biologist would like to start explore the genomics data from a couple of words that describe the “function” of a group of genes. It will also be useful to extract data of gene expression, and to search for the correlation between the gene expression pattern and the sequence features of those genes, in a single platform, such as Galaxy."

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positive feedback
by Ross Hardison 25 Sep '06

25 Sep '06

I unleashed a class of students on Galaxy, with options to do anything from working through tutorials to doing something advanced. I'm passing along some positive feedback. "Galaxy does not seem to be difficult to use, but since I was not sure what to try to do with a program that was new to me I decided to go though the tutorials. The tutorials are very helpful at explaining what Galaxy can be used to show. I think there are more features within Galaxy than I will ever use, however, one never knows." "I've never used Galaxy before, I thought doing the tutorial would be most beneficial to me. I thought the tutorial was very informative and done with a great deal of depth. I only wished that this was also available for the UCSC web browser. The tutorial in addition to the required reading was very helpful in understanding the use of Galaxy. As Blankenberg et al., (in press) explains the majority of users of the Galaxy program are biomedical researchers, most of whom are not familiar with basic programming. Hence in my option, such detailed tutorials are very helpful and a great timesaver. In particular, the way in which the screenplays are divided into specific groups a definitely less time consuming." "In general, I found all of the tools and functions of Galaxy simple to use and the interface easy to navigate. " "I found this tutorial and exercise very helpful and descriptive for using the program. I also watched screencasts 3A-3M. It was very helpful to have all the different tools in galaxy explained in detail and will come in handy for reference when using the program in the future. I especially found the screencasts on uploading data and encoding data very useful, such as the explanation of the different analysis groups. " Ross Hardison T. Ming Chu Professor of Biochemistry and Molecular Biology The Pennsylvania State University 304 Wartik Laboratory University Park, PA 16802 e-mail: rch8(a)psu.edu phone: 814-863-0113 FAX: 814-863-7024

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genomics
by Jeff Dole 19 Sep '06

19 Sep '06

Hi, I have a recent PhD in genetics from UC Davis. No one there, or at the UW Madison (where I took a class in "genomics") or at Harvard knows what it means. That has been readily admitted. Are you talking about plumbing or electricity? Jeff --

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test.g2.bx.psu.edu
by Ying Zhang 19 Sep '06

19 Sep '06

Hi, if you check the history stored as "7.26" under the account yuz111(a)psu.edu, you will find I encountered an error: "the scaffold for hg18 chr1 does not exist". Best, Ying

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improvement for pasting sequences
by Radek Szklarczyk 12 Sep '06

12 Sep '06

hi, i'd like to suggest an improvement to "Get Data/upload/paste sequence" option. Since it's hard to enter "tab" from keyboard on web pages (or when copy/pasting something from a web page), there should be an option "convert spaces to tabs". That would make it possible to enter BED format without manually replacing each space. radek --- Radek Szklarczyk, radek(a)cs.vu.nl, www.cs.vu.nl/~radek

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fail to load galaxy: test.g2.bx.psu
by Erika 08 Sep '06

08 Sep '06

i get this error: Internal Server Error i'm trying to load these pages: http://test.g2.bx.psu.edu/display?id=27069 http://test.g2.bx.psu.edu/display?id=27099 thanks! ********************************************************** E.M. Kvikstad Academic Computing Fellow IGDP Genetics Center for Comparative Genomics and Bioinformatics The Pennsylvania State University 208 Mueller Lab University Park, PA 16802 (814) 863-2185

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internal server error when trying to download file
by Radek Szklarczyk 07 Sep '06

07 Sep '06

I try to download alignments ( 606,582 lines, format: axt) and press "save" link. This gives "Internal server error" after a few seconds of waiting. Smaller history elems (like a bed file) can be downloaded without any problems. You can inspect my history, user:radek, history:arf, history elems giving errors:3-6 This used to work like a charm for even bigger files in older galaxies. cheers, radek --- Radek Szklarczyk, radek(a)cs.vu.nl, www.cs.vu.nl/~radek

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Convert Formats
by Liron Levkovitz 06 Sep '06

06 Sep '06

Hello, I'm trying to convert an AXT format file to FASTA . The AXT file include a table with 2,321,097 lines (It's the results of a blastz alignment between hg18 and mm8). Can you give me an estimation of how long it would take? Does it make since that it takes a few days? Thanks in advance, Liron Levkovitz Tel- Aviv University

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Data imports hang
by Ross Hardison 05 Sep '06

05 Sep '06

I encountered a new problem while going through a Galaxy example for my class, using Galaxy2.2. When importing data from the UCSC Main Table Browser, the history column does the usual count-down of "refreshing in 10 sec, 9 sec, 8 sec, ...", but once it stops at "refreshing in 1 sec". Then it just shows the spinning wheel indefinitely. Clicking on "refreshing in 1 sec" completes the import, and now you get the data in the history. - Ross Ross Hardison T. Ming Chu Professor of Biochemistry and Molecular Biology The Pennsylvania State University 304 Wartik Laboratory University Park, PA 16802 e-mail: rch8(a)psu.edu phone: 814-863-0113 FAX: 814-863-7024

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no mm5 sequence data in galaxy 2.2
by Radek Szklarczyk 04 Sep '06

04 Sep '06

when i try to download sequences for mm5 (uploaded bed file) i get an error: 4: Extract genomic DNA on data 2 An error occurred running this job: <font color="yellow">No sequences are available for musMus5</font> For hg17 it works correctly. --- Radek Szklarczyk, radek(a)cs.vu.nl, www.cs.vu.nl/~radek

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