Meeta Mistry

The vignette has been upgraded recently, need to review and see what additional features we can incorporate into our materials

update automation lesson for debugging

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look for intermediate bams, look at the job.out files, and also discuss sacct to see how jobs are doing maybe add and SBATCH directive to get an err file?

From Rory: "greylist regions are regions where the input exceeds a threshold, where peak-callers sometimes call spurious peaks. threshold is calculated by calculating depth over the input, sampling it repeatedly...

adding details pulldown to selected lessons

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This is an HTML tag taht would be useful for "try it on your own" sections, where the code is hidden initially but clicking on it will make it available...

add a note to peak calling for other types of analysis (broad peaks, ATAC-seq)

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Even the move to ChiP

score does not correspond with IDR

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Hi, I have run IDR and looking at my output, trying to understand why I have peaks that are IDR < 0.05 ( based on column 11) yet the corresponding...

replicates with haystack_bio

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How does haystack_bio handle replicates? For example, if each celltype in the example had 3 replicates therefore 3 input BAMs can we still run this?