March 2012 - 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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Re: [galaxy-user] Combining two workflows into one
by Peter Cock 19 Mar '12

19 Mar '12

You forgot to CC the mailin list. > On Mon, Mar 19, 2012 at 12:02 PM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote: >> On Mon, Mar 19, 2012 at 4:53 PM, Innocent Onsongo <onson001(a)umn.edu> wrote: >>> Galaxy Team, >>> >>> I would like to create a workflow by combining portions of two >>> different workflows. How do I do this in Galaxy? >>> >>> Thanks, >>> Getiria Onsongo >> >> One outline solution is as follows: >> >> (1) Start with an empty history. >> (2) Upload/import the input files >> (3) Run first workflow >> (4) Run second workflow >> (5) Save history as a new combined workflow >> (6) Edit new workflow to remove any redundant steps >> >> This is of course limited in functionality compared to what >> might be possible in a future version of Galaxy. >> >> Peter On Mon, Mar 19, 2012 at 5:05 PM, Innocent Onsongo <onson001(a)umn.edu> wrote: > I was hoping I could avoid re-running the two workflows since they > both take a relatively long time to run. Looks like I might have to do > it after all. Use smaller datasets? Ideally you would have a small test set covering positive and negative example. Or you can manually create the workflow in the workflow editor, starting from one of the existing ones and adding the new tools and connecting them together. Peter

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Combining two workflows into one
by Innocent Onsongo 19 Mar '12

19 Mar '12

Galaxy Team, I would like to create a workflow by combining portions of two different workflows. How do I do this in Galaxy? Thanks, Getiria Onsongo

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Dear Galaxy Developer, where is the "history/workflow" file stored in the local machine?
by 杨晨 18 Mar '12

18 Mar '12

Dear Galaxy Developer, where is the "history/workflow" file stored in the local machine? I mean the real file store in the disk instead of browser access. Thanks and Best regards -- Yang Chen Room 635, No.41 Building,320 Yueyang Road Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai,P.R.China Post Code:200032 Tel: 86-21-54921375

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Dear Galaxy Developer, where is the "history/workflow" file stored in the local machine?
by 杨晨 18 Mar '12

18 Mar '12

Dear Galaxy Developer, where is the "history/workflow" file stored in the local machine? Best regards -- Yang Chen Room 635, No.41 Building,320 Yueyang Road Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai,P.R.China Post Code:200032 Tel: 86-21-54921375 -------- Forwarding messages -------- From: yangchen(a)sibs.ac.cn Date: 2012-03-18 23:38:08 To: galaxy-user(a)bx.psu.edu Subject: Dear Galaxy Developer,where is the "history/workflow" flow stored in the local machine? Dear Galaxy Developer, where is the "history/workflow" flow stored in the local machine? Best regards -- Yang Chen Room 635, No.41 Building,320 Yueyang Road Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai,P.R.China Post Code:200032 Tel: 86-21-54921375

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Dear Galaxy Developer, where is the "history/workflow" flow stored in the local machine?
by yangchen＠sibs.ac.cn 18 Mar '12

18 Mar '12

Dear Galaxy Developer, where is the "history/workflow" flow stored in the local machine? Best regards -- Yang Chen Room 635, No.41 Building,320 Yueyang Road Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai,P.R.China Post Code:200032 Tel: 86-21-54921375

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wig file conversion
by Horvath, Lindsay 17 Mar '12

17 Mar '12

I am a PSU student at the College of Medicine. I have minimal bioinformatics and computer programing background. I was introduced to galaxy during televisied genomics course. I believe I am using galaxy on the cloud. I am trying to display ChIP-CHIP data on UCSC. I have downloaded the gff file (attached; NCBI/GEO # GSM413116) and uploaded it into galaxy (using get data; upload file). The initial publication converted gff file to wig file for upload into UCSC. I could not find this function in Galaxy so I tried converting to bed file instead (convert formats; gff-to-bed). When I do this and upload into UCSC I do not get the peak hight (score difference) at each site (column 6 of gff file; score--which appears to convert to all 0s in bed file), only the locations are annotated but not the score. Is there something I am doing wrong in the conversion to a bed file or alternatively is there a way to convert the intial gff file into a wig file? Any help would be greatly appreciated! Thanks, Lindsay Horvath

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fastq-MCF
by Benoît REMENANT 16 Mar '12

16 Mar '12

Hi all, Does someone know fastq-MCF? We are relatively newbies in analysing RNAseq results, and we would like to use the fastq-MCF program to trim our illumina sequences (based on quality score and adapters sequences) while keeping paired reads synchronized. Unfortunately, there are some parameters we did not understand, like -s (log scale for clip pct to threshold) and -t (% occurrence threshold before clipping). Does anyone can explain us what these parameters mean? Or when I can found useful information? And do you think we have to unable the PF filtering (and why)? Thank you very much in advance if someone can help us. Benoit

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Re: [galaxy-user] Read Length Distribution
by Jennifer Jackson 16 Mar '12

16 Mar '12

Hello, Other types of statistics can be generated with the "Join, Subtract and Group -> Group" tool, by adding an additional file manipulation. First run "Compute sequence length". Next run "Add column to an existing dataset" and set this to be the same value for all rows, "1" or something else simple. Nest, run "Group", with a group on the column containing the "Add column" value, and then click on "Add new Operation". Set "Type" to be "Mode" and "On column" to be the the sequence length. Very large files, usually when run with multiple operations, are occasionally to too large to run with this tool on the public main Galaxy instance. If this occurs, the first option is to simplify the query. If that doesn't work, then moving to a cloud instance would be the recommendation. Good luck with your project, Jen Galaxy team On 3/15/12 3:17 PM, Elad Firnberg wrote: > Hi Jen, > > Thank you, this was very helpful. Is there a way to get some more > statistical information such as the mode of read lengths? The summary > statistics tool only seems to provide the mean. > > Thank you, > Elad > > > On Thu, Mar 15, 2012 at 3:02 PM, Jennifer Jackson <jen(a)bx.psu.edu > <mailto:jen@bx.psu.edu>> wrote: > > Hi Elad, > > Start with the tool "FASTA manipulation -> Compute sequence length" > to generate a length value for each sequence. > > Next, use "Statistics -> Summary Statistics for any numerical > column" on the result to generate specific R function statistics > (see the tool form for which and how to enter the expression). > > To visualize the distribution, use "Graph/Display Data -> Histogram > of a numeric column". > > Hopefully this helps. > > Best, > > Jen > Galaxy team > > > On 3/15/12 9:24 AM, Elad Firnberg wrote: > > Hi, > > Is there a tool or easy way to obtain a read length distribution > on a > set of 454 reads in fasta format? I can't seem to find such a > tool in > Galaxy. > > Thank you, > Elad > > > > > > _____________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org <http://usegalaxy.org>. Please keep all > replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/__listinfo/galaxy-dev > <http://lists.bx.psu.edu/listinfo/galaxy-dev> > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > > > > -- > Chemical and Biomolecular Engineering > Johns Hopkins University > 3400 N. Charles St. Baltimore, MD 21218 > Tel# (410) 516-3937

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Read Length Distribution
by Elad Firnberg 15 Mar '12

15 Mar '12

Hi, Is there a tool or easy way to obtain a read length distribution on a set of 454 reads in fasta format? I can't seem to find such a tool in Galaxy. Thank you, Elad

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