Meeta Mistry

scores and p-values

3

Apologies, wasn't sure if this was the best place to post, but: 1. Is there a way of extracting a column of p-values along with the positions? 2. Is there...

coef vs contrast?

2

https://support.bioconductor.org/p/98833/#98837 See this post about using one or the other. Also see vignette for more info ---

question from the students, should we add this as a note? https://support.bioconductor.org/p/110307/

change sleuth to mike's new package ?

1

https://f1000research.com/articles/7-952/v1 Need to look into this!

In the note where we discuss other callers in the peak calling lesson we should link recent paper comparing tools (from Shannan's slides)

What do we do if a large percentage of reads map to blacklist regions (or many peaks are filtered out)? How do we interpret this? And what can be changed...

add a library preparation slide deck?

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could be useful since we have time, and we refer to various things i.e strandedness, RNA quality during the workshop