updated 16 months ago by
James W. MacDonald
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written 16 months ago by
Nikolay Ivanov
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Answer: Using both spike in and TMM normalizations in ChIP-seq samples
by
Gordon Smyth
43k
It is impossible to use both spike-in or TMM normalization. You must do one or the other. They replace each other, they cannot be combined.…
Comment: Best practice for quantifying sncRNA
by
ATpoint
▴
700
If the sequences are 20-something bp long then it appears logical to me to throw away any reads that are longer than that after adapter tri…
Comment: P value and Adj. P value showing N/A
by
ATpoint
▴
700
http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#why-are-some-p-values-set-to-na
As Mike says, you can be…
Comment: Using both spike in and TMM normalizations in ChIP-seq samples
by
ATpoint
▴
700
I just gave my two cents on spike-ins and normalization diagnostic over at biostars (see link below) which you may want to have a look at. …
Comment: Best practice for quantifying sncRNA
by
James W. MacDonald
57k
You may well get lots of protein coding genes, depending on what's in the transcripts file. Do note that most miRNA transcripts are complem…
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