User: sswanson

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sswanson20
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Posts by sswanson

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Comment: C: Why are there duplicate peaks in ENCODE ATAC-seq output?
... Found this long-ago version of my question, specifically referencing MACS2 rather than ATAC-seq: https://www.biostars.org/p/162788/ ...
written 8 weeks ago by sswanson20
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Comment: C: Why are there duplicate peaks in ENCODE ATAC-seq output?
... Based on a private communication with a colleague, I believe that, "You are correct, sir!" At the moment, I'm just trying to run the default Encode pipeline correctly, before I start messing about with custom peak-callers, read-trimmers, and aligners. Thanks! ...
written 8 weeks ago by sswanson20
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Why are there duplicate peaks in ENCODE ATAC-seq output?
... I've installed and run the current ENCODE-DCC ATAC-seq pipeline from GitHub. I have 2 replicates of ATAC-seq data. When I run the pipeline, regardless of which (blacklist-filtered) peak file I look at (rep1, rep2, or pooled), about 6% of the peak loci are repeated (but with different scores). Most a ...
encode atac-seq written 8 weeks ago by sswanson20 • updated 8 weeks ago by ATpoint42k

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