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

Analyzing Targeted Resequencing data with Galaxy
by Lali 05 Apr '11

05 Apr '11

Hi! I am having problems with my sequencing results, but I am a newbie at this; so I am thinking there is something wrong with my analysis. So far, I've tried Galaxy and CLC Workbench, but with CLC I could not align to the whole genome, only to individual chromosomes (maybe there is a way, but by the time the trial ended I had not found it). I used SureSelect capture kit and did single end sequencing on an Illumina. The files the lab sent me are FastQ Illumina 1.5 files, my samples were indexed, and I got a series of files each representing an Index. What would be the standard workflow for this kind of data? Which tools/settings? Does anyone have an example Galaxy workflow for preparing (clipping adapters, quality trimming) and mapping Targeted Resequencing Data? Is there a way to obtain a coverage report through Galaxy? Is it possible to ignore/discard the reads mapped when the coverage is below a certain threshold? I know, I know, a lot of things, but I am very lost. Any help is appreciated. L

5 5

Subject: Analyzing Targeted Resequencing data with> Galaxy
by Jackie Lighten 05 Apr '11

05 Apr '11

You can do all the quality filtering with Galaxy, but may involve various manipulations of the data. If I am not mistaken the "metagenomics" workflow may help you out a little. Its designed for 454 data but should give you an idea of how to go about things. There is a video tutorial on the site for this workflow. A good place for you to start, however, may be here: Subject: http://edwards.sdsu.edu/prinseq_beta/# Prinseq is easy to use and will give you a full break down of your raw data and enables you to filter by quality/length etc. FASTqc is an Illumina specialized preliminary analysis tool: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ I my self was not very impressed with CLC at all. It lacks very rudimentary yet critical functions. I am currently working on population amplicon data so couldn't really help you too much in the latest mapping to reference advances, but I found the Lasergene SEQman mapping and de-nova assembler much better than the CLC assembler. Good luck Jack On 11 > > Message: 6 > Date: Tue, 5 Apr 2011 08:44:06 +0200 > From: Lali <laurafe(a)gmail.com> > To: galaxy-user(a)lists.bx.psu.edu > Subject: [galaxy-user] Analyzing Targeted Resequencing data with > Galaxy > Message-ID: <BANLkTin1ShWLQQ46+mFFBcxS-dO1GJuw_A(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi! > I am having problems with my sequencing results, but I am a newbie at this; > so I am thinking there is something wrong with my analysis. So far, I've > tried Galaxy and CLC Workbench, but with CLC I could not align to the whole > genome, only to individual chromosomes (maybe there is a way, but by the > time the trial ended I had not found it). > > I used SureSelect capture kit and did single end sequencing on an Illumina. > The files the lab sent me are FastQ Illumina 1.5 files, my samples were > indexed, and I got a series of files each representing an Index. > > What would be the standard workflow for this kind of data? > Which tools/settings? > > Does anyone have an example Galaxy workflow for preparing (clipping > adapters, quality trimming) and mapping Targeted Resequencing Data? > > Is there a way to obtain a coverage report through Galaxy? > > Is it possible to ignore/discard the reads mapped when the coverage is below > a certain threshold? > > I know, I know, a lot of things, but I am very lost. > Any help is appreciated. > > L >

1 0

where to get indexes for mapping tools
by Yury Bukhman 04 Apr '11

04 Apr '11

Hi, we have set up a Galaxy server for internal use. We would like to provide indexes for NGS mapping tools for a set of organisms that are relevant to our research. While bowtie has a repository of such indexes, other tools, e.g. bwa, don't seem to have one, so we have to build our own. Is there a repository of pre-built indexes for all mapping tools supported by Galaxy somewhere? Thanks. Yury -- Yury V. Bukhman, Ph.D. Associate Scientist, Bioinformatics Great Lakes Bioenergy Research Center University of Wisconsin - Madison 445 Henry Mall, Rm. 513 Madison, WI 53706, USA Phone: 608-890-2680 Fax: 608-890-2427 Email: ybukhman(a)glbrc.wisc.edu

2 2

Published workflows in papers??
by Surya Saha 03 Apr '11

03 Apr '11

Hi, Are there any papers out there that have published links to Galaxy workflows that lets others run the workflows on new data or rerun the original analysis? Thanks -Surya

2 1

Around Pittsburgh on April 6? Attend the Intro to Galaxy Sessions @ Pitt
by Dave Clements 01 Apr '11

01 Apr '11

Hello all, Dan Blankenberg will be giving two workshops on Galaxy at the University of Pittsburgh on April 6. The presentations are open to the public. See below for details and please contact Dan, or Carrie Iwema at Pitt, if you have any questions. Thanks, Dave C. Intro to Galaxy http://galaxy.psu.edu/ Dan Blankenberg, PhD Center for Comparative Genomics & Bioinformatics Penn State University Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignments, compare genomic annotations, profile metagenomic samples & more... Wednesday 6th April *10 am – 12 pm Intro to Galaxy (general interest) * * * *2 pm - 4 pm Working w/NGS Data (advanced users) * University of Pittsburgh Falk Library Conference Room B You are welcome to bring your laptop. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Carrie L. Iwema, PhD, MLS Information Specialist in Molecular Biology Health Sciences Library System University of Pittsburgh 200 Scaife Hall 3550 Terrace St Pittsburgh, PA 15261 412-383-6887412-648-8819 (fax)iwema(a)pitt.eduwww.hsls.pitt.edu/molbio ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/

5 5

Re: [galaxy-user] Galaxy server-FTP
by Nate Coraor 01 Apr '11

01 Apr '11

Sher, Falak wrote: > Sorry I did not know there is some special software I need to use, could you help please ? Have you seen the instructions here?: https://bitbucket.org/galaxy/galaxy-central/wiki/UploadViaFTP Those example screenshots use Cyberduck. FileZilla is also a popular cross-platform FTP client. --nate > > ________________________________________ > From: Nate Coraor [nate(a)bx.psu.edu] > Sent: Thursday, March 31, 2011 11:36 PM > To: Sher, Falak > Cc: galaxy-user(a)lists.bx.psu.edu > Subject: Re: [galaxy-user] Galaxy server-FTP > > Sher, Falak wrote: > > HI > > I would like to use Galaxy server to upload files via FTP. I seek help for, log in to the FTP server at main.g2.bx.psu.edu. > > I dont see ftp log in option there. > > help please ? > > Hi Falak, > > What software are you using to try to connect via FTP? > > --nate > > > > > > > Falak > > > > ___________________________________________________________ > > 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/

1 0

Unsubscription
by Massimo 01 Apr '11

01 Apr '11

Hi, Is there a way to unsubscribe from Galaxy e-mail list? Please, let me know. Thanks Massimo Bionaz PhD Post-doctoral researcher Institute for Genomic Biology, University of Illinois 366 Animal Sciences Laboratory 1207 W. Gregory Dr. Urbana, IL 61801 USA Office Tel: 1-217-333-6189 Fax: 1-217-333-8286

2 1

Galaxy server-FTP
by Sher, Falak 31 Mar '11

31 Mar '11

HI I would like to use Galaxy server to upload files via FTP. I seek help for, log in to the FTP server at main.g2.bx.psu.edu. I dont see ftp log in option there. help please ? Falak

2 1