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

VERY URGENT PLEASE.
by Mrs Yomun Barakah 24 Apr '11

24 Apr '11

Dearest One, I am writting this mail to you with heavy sorrow in my heart.My name is Mrs Yomun Barakah.So do not be afraid.I am contacting you from my country Tunisia,i want to tell you this because i don't have any other option than to tell you as i was touched to open up to you. I am married to Mr.Asad Barakah,who worked with Tunisian embassy in Burkina-faso for nine years before he died in the year 2005.We were married for eleven years without a child.He died after a brief illness that lasted for only five days.Since his death i decided not to remarry,when my husband was alive he deposited the sum of us$ 8.2m(Eight million two hundred thousand dollars)in a bank in Ouagadougou the capital city of Burkina-faso in west Africa.presently this money is still in the bank.He made this money available for exportation of gold from Burkina-faso minning. Recently,my doctor told me that i would not last for the period of seven months due to canser problem.You see,whosoever that want to serve God must serve him in spirit and in truth because God is the most high,please always be prayerful all through your live. The one that disturbs me most is my cancer sickness.Having known my condition i decided to hand you over this money to take care of the less privileged people.You will utilise this money the way i am going to intruct you herein. I want you to take 30% of the total money for your personal use while 70% of the money will go to charity,people in the street and helping the orphanage. I don't have any child that will inherit this money and my husband relatives are not good,not even good at all because they are the one responsible for the death of my husband in other to have all my late husbands properties,and i don't want my husband's efforts to be used by those that conspired for his death. I grew up as an orphan and i don't have anybody as my family member,just to endeacour that the name of God is maintained.I am doing this so that God will forgive my sins and accept my soul,because this sicknrss have suffered me so much. As soon as i receive your reply i shall give you the contact of the bank in Burkina-faso,and i will send an authority letter to the bank that will prove you as the present beneficiary of the money in the bank.that is if you assure me that you will act accordingly as i intructed you herein. Hoping to receive your reply. Mrs Yomun Barakah. writting from Tunis.

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SAM to BAM conversion problem
by Kelkar, Hemant 21 Apr '11

21 Apr '11

Hello Galaxy Support, I generated an alignment with a "fastq groomed" illumina dataset using the "Map with BWA" tool in galaxy with the "C. elegans ce6" genome. Interestingly the results (when I click on the history name) say that the database used was "ce7". When I try to use the "SAM-to-BAM" tool, I am getting a "sequences are not currently available for specified build" error. Thanks, Hemant

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How to receive digest only?
by Yi Huang 21 Apr '11

21 Apr '11

Hi everyone, I'd like to know if i can receive digested mail only. Thanks Sincerely, John

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Workflows with run time parameters broken?
by Peter Cock 21 Apr '11

21 Apr '11

Hi all, I noticed a new problem with our local Galaxy (recently updated), but found it happens on the public installation too. I can edit workflows, and create run time parameters like ${Name} or ${Name with spaces}, but when I come to run the workflow I get an error: > Server Error >An error occurred. See the error logs for more information. > (Turn debug on to display exception reports here) e.g. This trivial example takes a FASTA file, does a minimum length filter, and tries to rename the output to a run time parameter string: http://main.g2.bx.psu.edu/u/peterjc/w/test-workflow-filter-fasta-min-length… Is this a known issue? I couldn't find a match on the bitbucket tracker. Thanks, Peter

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get wig file after tophat
by Ying Zhang 20 Apr '11

20 Apr '11

Hi: I am using tophat in galaxy to analyze my paired-end RNA-seq data and find out that after the tophat analysis, we can not get the wig file from it anymore which is used to be able to. Do you have any idea of how to still be able to get the wig file after tophat analysis? Thanks a lot! Best Ying Zhang, M.D., Ph.D. Postdoctoral Associate Department of Genetics, Yale University School of Medicine 300 Cedar Street,S320 New Haven, CT 06519 Tel: (203)737-2616 Fax: (203)737-2286

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Re: [galaxy-user] Normalization and plotting of RPKM/FPKM after cufflink
by vasu punj 20 Apr '11

20 Apr '11

Thanks Jeremy, This appear to be a useful function. Could you please enlist the steps in workflow to achieve the above visualization or alternatively point me to the URL where it is summarized please. I believe it will take Tophat out put Bam file and fpkm tracking file. I tried but I dont see track browser unless i convert to GTF file format. Further if you can point me how to get the slider window function as shown in snap shot that will be great. Good work Jeremy! Thanks. Vasu --- On Sun, 4/17/11, Jeremy Goecks <jeremy.goecks(a)emory.edu> wrote: From: Jeremy Goecks <jeremy.goecks(a)emory.edu> Subject: Re: Normalization an dplotting of RPKM/FPKM after cufflink To: "vasu punj" <punjv(a)yahoo.com> Cc: galaxy-user(a)bx.psu.edu Date: Sunday, April 17, 2011, 3:45 PM Vasu, > I want to include the following discussion in my message regarding use Bam files of Tophat to visualize reads either in IGV or Galaxy or other tools. > I want to find out if I can plot RPKM/FPKM normalized values > after running differential analysis in Cufflinks. Galaxy has a number of tools for analyzing numerical data; look under the menu items Statistics and Graph/Display Data for useful tools. If you're looking to plot FPKM values in addition to mapped reads from Tophat and Cufflinks transcripts, the Galaxy Tracks Browser might prove useful as it has filtering functionality so that you can move a slider to show/hide data based on FPKM values; its often useful to use the sliders for FPKM measures to get a sense of your data. See the attached screenshot for an example. Best, J.

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ce6/WS190 bowtie index
by giovanni stefani 20 Apr '11

20 Apr '11

Hello everybody, I would like to download the C. elegans ce6/WS190 bowtie index (six .ebwt files and the make_c_elegans_ws120.sh) that is in use in galaxy Tophat as reference genome. Is that possible, and how do I go about that? Thank you very much, Giovanni

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Suppress reporting hit number
by Hsin-l (Sam) Chiang 20 Apr '11

20 Apr '11

Hi, I used the Megablast function (in the NGS: Mapping\ROCHE-454\) to analyze my FASTA sequences against nt database and it worked fine for me. However, it generated 56,804 hits although my query has only 1000 sequences. I am wondering is there any way to suppress the number of reported alignments to just one best hit per sequence? (In the local BLAST there are parameters such as -K1 -v 1 -b 1 to do so, but I can't find similar options in Galaxy). Many thanks! Sam

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Combining tables with different numbers of columns
by Peter Cock 20 Apr '11

20 Apr '11

Hi all, I'm having a little trouble understanding the best way to perform some tabular file manipulations in Galaxy. I have several tabular files, which contain different numbers of columns, which I want to combine using a single column containing an identifier (which must match for the rows to be combined). e.g. File 1 contains, c1 = ID c2 = Score1a File 2 contains, c1 = ID c2 = Score2a c3 = Score2b c4 = Score2c File 3 contains, c1 = ID c2 = Score3a c3 = Score3b Desired combined file containing: c1 = ID c2 = Score1a c3 = Score2a c4 = Score2b c4 = Score2c c6 = Score3a c7 = Score3b I have worked out how to do this with two calls to the "Join two Datasets" tool, but this results in the repetition of the join column (ID in this example), so a final clean-up is required using the "Cut" tool (which breaks the column assignments). The more flexible "Column Join" tool would let me combine an arbitrary number of files, but is designed for input files containing the same column structure. Is there a better way to do this with Galaxy as it stands? Alternatively, would adding an option to the "Join two Datasets" tool not to bother with the redundant column be widely useful? Peter

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Re: [galaxy-user] Workflows with run time parameters broken?
by Peter Cock 20 Apr '11

20 Apr '11

On Wed, Apr 20, 2011 at 3:44 PM, Douglas Allan <dwallan(a)interchange.ubc.ca> wrote: > get me off this email list > Please don't hijack existing threads. See: http://lists.bx.psu.edu/pipermail/galaxy-user/2011-April/002281.html and: http://lists.bx.psu.edu/pipermail/galaxy-user/2011-April/002439.html Peter

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