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Comment: More regions in union when increasing DBA$config$mergeOverlap
by
Ian D.
▴
70
Hello. Thanks for the reply.
Sorry about this. My testing is telling me that 1 is the default (a gap), not -1 (1bp overlap). Negative …
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★
4.1k
> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level
edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq
by
james.zhang20
•
0
Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
Answer: Deseq2 and Normalization of RNA sequencing data
by
ATpoint
★
4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★
4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
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