questions about vast-tools align and diff

vastgroup / vast-tools

A toolset for profiling alternative splicing events in RNA-Seq data.

MIT License

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questions about vast-tools align and diff #44

Closed Rahel14350 closed 9 years ago

Rahel14350 commented 9 years ago

Dear Tim, -As I have 10 levels of data and afterwards I need to do differential splicing analysis on the output data. Do you still recommend me to use Diff? Or is it possible to import IR counts or exon skipped counts in DESeq2 and do the differential analysis there, if yes which column in each output showing the row count for each one?

-Sorry for many question, but your answers will help me a lot. Many thanks in advance, Rahel

timbitz commented 9 years ago

As is stated in the documentation, you can use vast-tools diff for any number of replicates, but can only make a comparison between two groups at a time -a rep1,rep2,...,repN -b repA,repB,repC.

Regarding DEseq/DEXseq, Again-- there are fundamental differences between vast-tools vs. DESeq/DEXseq and their input/output are not compatible (nor can the be coerced to be) in any way shape or form.