June 2013 - galaxy-user - lists.galaxyproject.org

Help with Summary Statistics
by D. A. Cowart 23 May '14

23 May '14

Hello, I am attempting to use Galaxy to calculate the mean sequence read length and identify the range of read lengths for my 454 data. The data has already been organized and sorted by species. The format of the data is as follows: >HD4AU5D01BHBCQCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC >HD4AU5D01A093MCTCTGTCGCTCTGTCTCTCTTCTCTCTCTCTCTCTCT etc...for each species I have attempted to use the "Summary Statistics" button, however it appears to only be for numerical data and not sequence data. Is this tool/task available via Galaxy? Thank you, Dominique Cowart User name: dac330

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SNP finding
by Xiefan Fang 03 Dec '13

03 Dec '13

Dear galaxy users, We have done deep sequencing on some known genomic loci using Hiseq2000. I have already mapped the reads to the reference sequences by using Galaxy. In the next step, I want to find SNPs and calculate the SNP percentage within the reads. There are 500,000 to 1,000,000 reads per biological sample. Can I do it with galaxy? If not, is there other programs available in windows? Considering that I am not very familiar with programming. Thanks, Xiefan University of Florida

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analysing pooled data with FreeBayes
by Nicola Smith 24 Jul '13

24 Jul '13

Hi, I am new to this and I hope someone can help. I have pooled sequencing data that I am trying to analyse using Galaxy. I've done quite a bit of online searching and it seems that FreeBayes should be able to do this, if I select "set population", click the "Assume that samples result from pooled sequencing" option and change the ploidy to nx2 (number of alleles, where n is the number of subjects and the organism is diploid). However, whenever I do this I get an error: usually just "Killed" I was originally setting my polidy rather high (190 as I have 95 subjects pooled), so I wondered if this was the problem, however, it fails if I do a ploidy of only 4 too. I've tried various things to try to see where I am going wrong: All with the same BAM file: Set population model options: Do not set --> works Set population model options: set, Assume that samples result from pooled sequencing: not ticked, Default ploidy for the analysis: 2 --> works Set population model options: set, Assume that samples result from pooled sequencing: ticked, Default ploidy for the analysis: 2 --> works Set population model options: set, Assume that samples result from pooled sequencing: ticked, Default ploidy for the analysis: 4 --> fails (killed) Set population model options: set, Assume that samples result from pooled sequencing: ticked, Default ploidy for the analysis: 10 --> fails (killed) Set population model options: set, Assume that samples result from pooled sequencing: ticked, Default ploidy for the analysis: 10 --> fails (killed) It seems that it is the ploidy part that I am doing wrong, as it works with pooled data but ploidy of 2. I'm sure I have to change the ploidy though, or else how does the program know how many subjects are in the pool? Also, everywhere that I've ready says you have to change the ploidy. I apologise if my question is naive. As I said, I am new to Galaxy and this is the first thing I am trying to do! Any help / suggestions would be appreciated, Thanks, Nic

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barcode splitter files web based
by Ann Holtz-Morris, M.S. 11 Jul '13

11 Jul '13

HI, I'm trying to use the output files from barcode splitter. I know that the command line as some wrappers made that take the output files and puts them in the history. Is there anything similar for output files but for us biologists who don't do command line? J Thanks, Ann CONFIDENTIALITY NOTICE: This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you.

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elandmulti format
by Murphy, Theresa 09 Jul '13

09 Jul '13

Using the Galaxy public server, Is it possible to do peak calling using MACS on Bowtie mapped paired end reads if I do not have access to ELAND to generate ELANDMULTI format. The illumina reads were originally downloaded from the SRA database rather than being generated in house. Is it possible to convert the Bowtie output to ELANDMULTI format? Thanks, Theresa Murphy The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.

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Problem with ftp server?
by Katrien M. Devos 01 Jul '13

01 Jul '13

I successfully uploaded files to the main Galaxy server this morning using ftp. However, any attempts to upload files since around noon have failed. I get a 'Could not connect to server' error when trying to connect to main.g2.bx.psu.edu uisng FileZilla. Any suggestions? Thank you. Katrien -- Katrien M. Devos Dept. of Crop and Soil Sciences & Dept. of Plant Biology University of Georgia Athens, GA 30602 USA Tel: (706) 542-0925 Fax: (706) 542-0914 E-mail: kdevos(a)uga.edu

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(no subject)
by Dave Clements 30 Jun '13

30 Jun '13

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Re: [galaxy-user] galaxy-user Digest, Vol 84, Issue 27
by Batool Akhtar-Zaidi 28 Jun '13

28 Jun '13

Please unsubscribe Sent from my iPhone On Jun 28, 2013, at 12:01 PM, "galaxy-user-request(a)lists.bx.psu.edu" <galaxy-user-request(a)lists.bx.psu.edu> wrote: > Send galaxy-user mailing list submissions to > galaxy-user(a)lists.bx.psu.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.bx.psu.edu/listinfo/galaxy-user > or, via email, send a message with subject or body 'help' to > galaxy-user-request(a)lists.bx.psu.edu > > You can reach the person managing the list at > galaxy-user-owner(a)lists.bx.psu.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of galaxy-user digest..." > > > HEY! This is important! If you reply to a thread in a digest, please > 1. Change the subject of your response from "Galaxy-user Digest Vol ..." to the original subject for the thread. > 2. Strip out everything else in the digest that is not part of the thread you are responding to. > > Why? > 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. > 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. > > Today's Topics: > > 1. Re: gft annotation files (Jennifer Jackson) > 2. Re: Pause function please (Jennifer Jackson) > 3. Problem with ftp server? (Katrien M. Devos) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 27 Jun 2013 11:12:38 -0700 > From: Jennifer Jackson <jen(a)bx.psu.edu> > To: Vijay Kumar <nayaganviji(a)gmail.com> > Cc: galaxy-user(a)bx.psu.edu > Subject: Re: [galaxy-user] gft annotation files > Message-ID: <51CC8096.2030802(a)bx.psu.edu> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Hello, > > The UCSC Table browser can be used to extract a GTF file formatted > dataset. See the tool "Get Data -> UCSC Main". The output format is one > of the choices at the bottom of the tool UCSC form and there is a user > guide below that at the UCSC web site that details how-to for queries. > > Best, > > Jen > Galaxy team > > > On 6/27/13 4:35 AM, Vijay Kumar wrote: >> Dear sir, >> any one suggest me where i download reference annotation gft files for >> zebra finch . i tried ucsc site, but i donot know exact place to get >> gft files. thank u sir.......... >> >> >> ___________________________________________________________ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at 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 >> >> To manage your subscriptions to this and other Galaxy lists, >> please use the interface at: >> >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> >> http://galaxyproject.org/search/mailinglists/ > > -- > Jennifer Hillman-Jackson > Galaxy Support and Training > http://galaxyproject.org > >

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Pause function please
by Ann Holtz-Morris, M.S. 27 Jun '13

27 Jun '13

Hi, I read https://www.google.com/url?q=http://dev.list.galaxyproject.org/Can-t-find-n… <https://www.google.com/url?q=http://dev.list.galaxyproject.org/Can-t-find-n…> &sa=U&ei=KFzLUaHFCaGcjALSq4GQCw&ved=0CAcQFjAA&client=internal-uds-cse&usg=AFQjCNHSziHrbCCmumvDDUtmAeW9RvLRdg with interest. I would also like a Pause function as a toggle on/off so I can stop look at the data being generated. I'm running a BWA alignment that's been working now for almost 48 hours. It's a decent sized data set but it had a very low quality second sequencing read. I've quality trimmed and length filtered. It ended up being only ~50% of the # of reads in Read1. I'd love to be able to pause it and see if the data set is behaving as expected. Thanks, Ann Ann Holtz-Morris SRA III de Jong Laboratory 510-428-3885 x 5715 aholtzmorris(a)chori.org Shipping and Mailing Address Attention: Ann Holtz-Morris CHORI-BACPAC Resources BLMR Bldg. 747 52nd St. Oakland, CA 94609-1809 CONFIDENTIALITY NOTICE: This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you.

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gft annotation files
by Vijay Kumar 27 Jun '13

27 Jun '13

Dear sir, any one suggest me where i download reference annotation gft files for zebra finch . i tried ucsc site, but i donot know exact place to get gft files. thank u sir..........

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