SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 28
Search took 0.00 seconds.
Search: Posts Made By: jgoecks
Forum: Academic/Non-Profit Jobs 03-18-2014, 12:19 PM
Replies: 0
Views: 885
Posted By jgoecks
Software Engineer for the Galaxy Project

The Interactive Genomics Lab at George Washington University’s Computational Biology Institute is looking to fill an unusual and exciting software engineering position working on the Galaxy project...
Forum: Academic/Non-Profit Jobs 02-24-2014, 11:03 AM
Replies: 0
Views: 822
Posted By jgoecks
Postdoctoral Scholars in Biological Visualization @ George Washington University

Overview

The Interactive Genomics Lab at George Washington University (http://jeremygoecks.com) is recruiting creative and motivated postdoctoral scholars interested in doing biological...
Forum: Academic/Non-Profit Jobs 01-20-2014, 09:10 AM
Replies: 0
Views: 925
Posted By jgoecks
Postdoctoral Scholars in Bioinformatics/Computational Biology @ George Washington U

Overview

The Interactive Genomics Lab at George Washington University (http://jeremygoecks.com) is recruiting creative and motivated postdoctoral scholars interested in doing bioinformatics and...
Forum: Bioinformatics 10-27-2013, 06:26 AM
Replies: 10
Views: 8,195
Posted By jgoecks
@ASL: *I do not think sFTP to usegalaxy.org...

@ASL:

*I do not think sFTP to usegalaxy.org is implemented yet, but it is coming; for now you should use FTP
*instructions for configuring FTP on local instance are here:...
Forum: RNA Sequencing 11-28-2012, 02:24 PM
Replies: 27
Views: 47,726
Posted By jgoecks
@Peppe re: JGI gene annotation No need to...

@Peppe re: JGI gene annotation

No need to run that workflow on the annotation in your case. Just make sure that your gene annotation's contig names (column 1) match the names in your genome's...
Forum: RNA Sequencing 11-28-2012, 02:22 PM
Replies: 27
Views: 47,726
Posted By jgoecks
@Peppe Cummerbund is the preferred option...

@Peppe

Cummerbund is the preferred option for visualizing Cuffdiff output, but it's not yet integrated into Galaxy.

However, there is a scatterplot that's handy for visualizing FPKM data for...
Forum: RNA Sequencing 11-19-2012, 09:40 AM
Replies: 27
Views: 47,726
Posted By jgoecks
@Peppe I assume you're using the public...

@Peppe

I assume you're using the public Galaxy server at https://main.g2.bx.psu.edu/ , yes?

If so:

(a) Galaxy will work fine on Windows, though you'll want to you Firefox or Chrome as your...
Forum: RNA Sequencing 08-17-2012, 08:41 AM
Replies: 27
Views: 47,726
Posted By jgoecks
Your data is almost certainly not solexa format;...

Your data is almost certainly not solexa format; most newer Illumina data is already fastqsanger, in which case the groomer is not needed.

See the Wikipedia entry for FASTQ for more details:
...
Forum: RNA Sequencing 08-13-2012, 01:59 PM
Replies: 27
Views: 47,726
Posted By jgoecks
Trimming PE reads in Galaxy

@weijenc

My suggestion for trimming paired-end reads in Galaxy is:

(1) Join them using the FASTQ joiner;
(2) Filter them using the Filter FASTQ tool;
(3) Split them using the FASTQ splitter....
Forum: Bioinformatics 10-03-2011, 07:33 PM
Replies: 10
Views: 6,525
Posted By jgoecks
Kunio, Here are instructions for setting up...

Kunio,

Here are instructions for setting up indices for NGS tools:

http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup

Good luck,
J.
Forum: Bioinformatics 10-03-2011, 06:25 PM
Replies: 10
Views: 6,525
Posted By jgoecks
All, You'll need to put Bowtie--and other...

All,

You'll need to put Bowtie--and other tools that you want to use--in your user's path. Something like:

% bash
% export PATH=$PATH:/path/to/bowtie/

should do the trick on most systems....
Forum: RNA Sequencing 08-16-2011, 04:46 AM
Replies: 27
Views: 47,726
Posted By jgoecks
GenoMax, Quotas on our public instance are a...

GenoMax,

Quotas on our public instance are a new feature (within the last couple weeks) and are being phased in slowly. Moreover, we're still in process of determining what the quotas should be;...
Forum: RNA Sequencing 08-10-2011, 01:07 PM
Replies: 27
Views: 47,726
Posted By jgoecks
Quan, The answers to your questions depend...

Quan,

The answers to your questions depend on whether you're using our public server or running Galaxy locally/on the cloud.

If you're using our public server (main.g2.bx.psu.edu):

(1) you...
Forum: RNA Sequencing 05-02-2011, 05:30 AM
Replies: 27
Views: 47,726
Posted By jgoecks
@neo Galaxy makes it relatively easy to move...

@neo

Galaxy makes it relatively easy to move files from one instance to another:

(1) for the dataset that you want to move, right click on the save (disk) icon next to the dataset and copy its...
Forum: RNA Sequencing 05-01-2011, 08:39 AM
Replies: 27
Views: 47,726
Posted By jgoecks
@neo, rQuant was developed by Gunnar...

@neo,

rQuant was developed by Gunnar Ratsch's Lab and is available via their public Galaxy instance at http://galaxy.tuebingen.mpg.de/ Questions should be directed towards them (Help menu -->...
Forum: Bioinformatics 04-13-2011, 06:10 AM
Replies: 4
Views: 6,306
Posted By jgoecks
Yes, I am seeing this problem in Tophat v1.2.0 as...

Yes, I am seeing this problem in Tophat v1.2.0 as well, using samtools 0.1.12a. I have not been able to fix it as of yet; any help would be greatly appreciated.
Forum: Bioinformatics 04-07-2011, 06:31 PM
Replies: 10
Views: 6,525
Posted By jgoecks
Hi all, Galaxy does not include Bowtie in...

Hi all,

Galaxy does not include Bowtie in its distribution. You'll need to download and install Bowtie in order to run it using Galaxy. More information about installing Bowtie for Galaxy can be...
Forum: Bioinformatics 03-21-2011, 12:53 PM
Replies: 2
Views: 1,810
Posted By jgoecks
Hi Hammy, Sorry for the slow reply. The...

Hi Hammy,

Sorry for the slow reply.

The format required for the len file is:

--
<contig_1_name><tab><contig_1_length>
...
<contig_N_name><tab><contig_N_length>
Forum: Bioinformatics 01-28-2011, 10:56 AM
Replies: 10
Views: 2,686
Posted By jgoecks
Seeing this error in v0.9.3, no reference annotation

I'm seeing this error in v0.9.3 using a Cufflinks GTF file that was generated without a reference annotation:

--
Error: no XLocus created for transcript CUFF.240853.1 (file M_californicus.gtf)...
Forum: RNA Sequencing 01-13-2011, 06:32 AM
Replies: 4
Views: 2,614
Posted By jgoecks
There is also a group devoted to trans-abyss: ...

There is also a group devoted to trans-abyss:

http://groups.google.com/group/trans-abyss

Best,
J.
Forum: RNA Sequencing 12-16-2010, 05:21 AM
Replies: 27
Views: 47,726
Posted By jgoecks
Hello, (1) Clicking on the save icon (the...

Hello,

(1) Clicking on the save icon (the disk) rather than the arrow will download the BAM file rather than the index. (This is a recent UI bug, and we've fixed it in our codebase; you'll see...
Forum: Bioinformatics 12-08-2010, 07:33 AM
Replies: 6
Views: 4,954
Posted By jgoecks
Yes, that worked. Thanks!

Yes, that worked. Thanks!
Forum: Bioinformatics 12-08-2010, 06:33 AM
Replies: 6
Views: 4,954
Posted By jgoecks
Bump. I'll still seeing this problem in version...

Bump. I'll still seeing this problem in version 0.9.1 Any ideas or fixes?

Thanks,
J.
Forum: RNA Sequencing 11-29-2010, 01:06 PM
Replies: 27
Views: 47,726
Posted By jgoecks
Free & Open Environment for RNA-seq analysis: Galaxy (http://usegalaxy.org)

The Galaxy Team is excited to announce that the first free public resource for RNA-seq analysis is now available through the Galaxy public server at http://usegalaxy.org

Galaxy now supports both...
Forum: Bioinformatics 11-16-2010, 12:52 PM
Replies: 10
Views: 8,195
Posted By jgoecks
Galaxy now has integrated FTP server

Hi all,

With Galaxy's most recent update, you can now FTP your files directly to Galaxy rather than uploading via a web browser. While this isn't perfect, it's definitely better than most other...
Showing results 1 to 25 of 28

 


All times are GMT -8. The time now is 02:03 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO