RNA-seq analysis-feedback on a commercial package

[rnaseq]

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.

[NextGenSeq]

This sounds more like spam to me than a real user.

[ECO]

NGS, I agree. However the posts are coming from an IP at (redacted) , so I'm going to let it stay up for now.

[rnaseq]

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.

[ECO]

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.

[pareje]

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.

[steven]

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.

[Strand SI]

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