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Has anyone used GeneSifter for RNA-Seq data? It looks like it takes care of mapping, splicing detection and visualization. There's a lot of good functions there, but I'm not sure how well they're implemented.
My first concern is that uploading the full csfasta to their web servers will take a long time.
My second concern is that the statistics they list are basically just variations on the t-test, which in our experience don't work really well for RNA-Seq data. We've got a data normalization process and corresponding statistical test that works quite well. GeneSifter appears to allow for extensions, and I'm wondering if it allows for that level of customization.
My only other question (not so much a concern) is how their algorithms differ from those in the open source alternatives.
My first concern is that uploading the full csfasta to their web servers will take a long time.
My second concern is that the statistics they list are basically just variations on the t-test, which in our experience don't work really well for RNA-Seq data. We've got a data normalization process and corresponding statistical test that works quite well. GeneSifter appears to allow for extensions, and I'm wondering if it allows for that level of customization.
My only other question (not so much a concern) is how their algorithms differ from those in the open source alternatives.