Intro-to-ChIPseq-flipped
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hbctraining
Dear, How do you incorporate DNA E.coli Spike in normalization into Macs2 peak calling? I'm struggling with finding a good way to use a scaling factor. Kind regards, Sarah-Lee
There seems to be some debate about whether IgG or chromatin input is best for negative control in Cut and Run. A quick google seems to suggest that most people...
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 multiQC snippet so people know that they can aggregate QC across samples.
In variant calling we use string manipulation `cd /n/scratch/users/${USER:0:1}/$USER` Can we include this in our automation lesson? https://github.com/hbctraining/variant_analysis/blob/main/lessons/01_data_organization.md#a-quick-explanation-on-the-use-of-user01
there is an image in the bowtie2 section (right under a section where we talk about soft-clipping) whihc is not relevant and difficult to explain. let's remove it and/or maybe...