c) if you can create an appropriate input matrix (read counts by exon
or other contig for each sample eg), the Principal Component Analysis
tool might be helpful (library size normalization is one devil that
lies in the detail and it's not quite the same as MDS - see below)
I like starting
Hi Ross,
Thanks for the suggestions. I'm aware that this is not really a
Galaxy-specific question, and I've been browsing through SeqAnswers and
found a couple of suggestions using edgeR or DESeq, but nothing for Tuxedo
suite. However, I have no experience with either of these tools, so I was
Hi Dave,
This is an interesting and non-trivial question that extends well
beyond Galaxy - and there's no simple solution AFAIK
Defining an 'outlier' tends to boil down to subjective judgement in
most real cases I've seen.
EG: see
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