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.
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.
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