SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 11 of 11
Search took 0.00 seconds.
Search: Posts Made By: jgoecks
Forum: RNA Sequencing 11-28-2012, 03:24 PM
Replies: 27
Views: 59,962
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, 03:22 PM
Replies: 27
Views: 59,962
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, 10:40 AM
Replies: 27
Views: 59,962
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, 09:41 AM
Replies: 27
Views: 59,962
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, 02:59 PM
Replies: 27
Views: 59,962
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: RNA Sequencing 08-16-2011, 05:46 AM
Replies: 27
Views: 59,962
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, 02:07 PM
Replies: 27
Views: 59,962
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, 06:30 AM
Replies: 27
Views: 59,962
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, 09:39 AM
Replies: 27
Views: 59,962
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: RNA Sequencing 12-16-2010, 06:21 AM
Replies: 27
Views: 59,962
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: RNA Sequencing 11-29-2010, 02:06 PM
Replies: 27
Views: 59,962
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...
Showing results 1 to 11 of 11

 


All times are GMT -8. The time now is 11:56 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO