SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
RNA-Seq: DEB: A web interface for RNA-seq digital gene expression analysis. Newsbot! Literature Watch 6 02-06-2012 04:55 AM
RNA-Seq: ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count da Newsbot! Literature Watch 0 11-18-2011 02:20 AM
RNA-Seq: Comparative Analysis of RNA-Seq Alignment Algorithms and the RNA-Seq Unified Newsbot! Literature Watch 3 07-31-2011 07:08 PM
ChIP-Seq: ChIP-seq Analysis in R (CSAR): An R package for the statistical detection o Newsbot! Literature Watch 0 05-11-2011 03:40 AM
Help: I need to speak to an expert in commercial DNA analysis applications Nomijill Bioinformatics 1 12-04-2009 04:42 AM

Reply
 
Thread Tools
Old 04-04-2011, 09:23 AM   #1
rnaseq
Junior Member
 
Location: washington

Join Date: Dec 2009
Posts: 7
Default RNA-seq analysis-feedback on a commercial package

I had seen several commercial packages mentioned on this forum for analysing RNA-seq and DNA-seq data. This post is for fellow biologists with a ton of RNA-seq data and no bioinformatics/math background. Our lab purchased a license for Avadis a few months ago. We've been using it mainly for RNA-seq analysis and we're extremely pleased with the package. I agree with a previous post that the manual although thorough is not user-friendly. But this was a non-issue since their tech support is fabulous and the package itself turned out to be really easy to use. Also, unlike another commercial package that our neighboring lab purchased, the Avadis guys didn't disappear after we paid for our license. They've arranged 3 private webexes for our lab where they've answered every qn we had-if you need a lot of hand-holding (our group did) they do a great job. Another impressive point about their tech team is that they have worked with us to find analysis options based on our needs (by creating additional filters that can be easily imported into the workflow). About the workflow itself, all you need are prealigned files (BAM or SAM) and it's easy to do the basic differential expression analysis. There are filters that can be chained to process the genelists. Also, they have a sleek genome browser, link-outs to pathways and clustering options. It is easy to create venn diagrams to compare differentially expressed genelists between experiments. Overall, it is a reasonably priced package that is quite fast and our computers have never crashed in the 4 months that we've worked with it.
I would recommend this package to anybody that is in the same boat as I was last year-a biologist with a ton of RNA-seq data and at the mercy of an under-staffed bioinformatics core. An additional plus for people that have used Genespring for microarray analysis-this package was developed by the same team and is very similar in terms of organization and workflow.
rnaseq is offline   Reply With Quote
Old 04-04-2011, 11:51 AM   #2
NextGenSeq
Senior Member
 
Location: USA

Join Date: Apr 2009
Posts: 482
Default

This sounds more like spam to me than a real user.
NextGenSeq is offline   Reply With Quote
Old 04-04-2011, 12:46 PM   #3
ECO
--Site Admin--
 
Location: SF Bay Area, CA, USA

Join Date: Oct 2007
Posts: 1,352
Default

NGS, I agree. However the posts are coming from an IP at (redacted) , so I'm going to let it stay up for now.
ECO is offline   Reply With Quote
Old 04-04-2011, 04:31 PM   #4
rnaseq
Junior Member
 
Location: washington

Join Date: Dec 2009
Posts: 7
Default reply to "seems like spam"

You can go back and read my previous posts over hte last 2 yrs. I've wasted a lot of time because I didn't have any way of analyzing my data. I thought I'd share my feedback on this package. Won't be wasting my time doing this anymore.
rnaseq is offline   Reply With Quote
Old 04-04-2011, 05:49 PM   #5
ECO
--Site Admin--
 
Location: SF Bay Area, CA, USA

Join Date: Oct 2007
Posts: 1,352
Default

rnaseq...apologies for what seems to clearly be a false positive.

We've had many instances of subtly disguised commercial posts so we're rightfully cautious...the lack of carriage returns probably didn't help our obviously flawed "algorithm".

Please don't take this as how helpful users are treated here...I know for a fact that everyone appreciates your time and review.
ECO is offline   Reply With Quote
Old 04-05-2011, 01:44 AM   #6
pareje
Junior Member
 
Location: Israel

Join Date: Aug 2010
Posts: 2
Default I appreciate your effort in this tool evaluation

rnaseq, thank you for the post, I was actually looking for real users and your input very much helps in making our decision about which is the best tool to use.
pareje is offline   Reply With Quote
Old 04-05-2011, 03:20 AM   #7
steven
Senior Member
 
Location: Southern France

Join Date: Aug 2009
Posts: 269
Default

Quote:
Originally Posted by pareje View Post
rnaseq, thank you for the post, I was actually looking for real users and your input very much helps in making our decision about which is the best tool to use.
Sounds like a spam too..
just kidding
or maybe not?

BTW, thanks and congratulations to the admins and moderators for the good job all these years.
steven is offline   Reply With Quote
Old 04-05-2011, 10:03 AM   #8
Strand SI
The Avadis NGS Team
 
Location: All over the World

Join Date: Feb 2011
Posts: 26
Default Thanks for the feedback

Thank you to 'rnaseq' for the positive review -- we were pleasantly surprised to see this. Our engineering and support teams work around-the-clock to build and maintain Avadis NGS, and were uplifted to read this post.

We are working on making the user manual more easy to read, so please continue to give us specific feedback on the user manual. It is a little
tricky to take an advanced NGS algorithm, and explain it in plain english, but we are working hard on it!

The Avadis NGS Team
http://avadis-ngs.com

Last edited by Strand SI; 04-05-2011 at 08:08 PM.
Strand SI is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 04:34 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO