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@@ -599,19 +599,25 @@ Methods
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\end_layout
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\begin_layout Standard
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-A reproducible workflow
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-\begin_inset CommandInset citation
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-LatexCommand cite
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-key "gh-cd4-csaw"
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-literal "false"
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+\begin_inset Flex TODO Note (inline)
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+status open
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+
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+\begin_layout Plain Layout
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+Look up some more details from the papers (e.g.
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+ activation method).
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+\end_layout
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\end_inset
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- was written to analyze the raw ChIP-seq and RNA-seq data from previous
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- studies
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+
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+\end_layout
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+
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+\begin_layout Standard
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+A reproducible workflow was written to analyze the raw ChIP-seq and RNA-seq
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+ data from previous studies
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\begin_inset CommandInset citation
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LatexCommand cite
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-key "LaMere2016,LaMere2017"
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+key "LaMere2016,LaMere2017,gh-cd4-csaw"
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literal "true"
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\end_inset
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@@ -630,6 +636,23 @@ literal "true"
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The result was 32 samples for each assay.
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\end_layout
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+\begin_layout Subsection
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+ChIP-seq alignment and peak calling
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+\end_layout
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+
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+\begin_layout Standard
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+\begin_inset Flex TODO Note (inline)
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+status open
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+
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+\begin_layout Plain Layout
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+All info from this subsection belongs in other subsections.
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+\end_layout
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+
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+\end_inset
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+
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+
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+\end_layout
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+
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\begin_layout Standard
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Sequence reads were retrieved from the Sequence Read Archive (SRA)
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\begin_inset CommandInset citation
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@@ -684,7 +707,8 @@ literal "false"
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.
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Peaks are also called separately using MACS, but MACS was determined to
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- be a poor fit for the data, and these peak calls are not used further
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+ be a poor fit for the data, and these peak calls are not used in any further
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+ analyses
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\begin_inset CommandInset citation
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LatexCommand cite
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key "Zhang2008"
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@@ -695,39 +719,6 @@ literal "false"
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.
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\end_layout
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-\begin_layout Itemize
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-Re-analyze previously published CD4 ChIP-seq & RNA-seq data
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-\end_layout
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-
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-\begin_deeper
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-\begin_layout Itemize
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-Completely reimplement analysis from scratch as a reproducible workflow
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-\end_layout
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-
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-\begin_layout Itemize
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-Use newly published methods & algorithms not available during the original
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- analysis: SICER, csaw, MOFA
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-\begin_inset CommandInset citation
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-LatexCommand cite
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-key "Argelaguet2018"
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-literal "false"
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-
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-\end_inset
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-
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-, ComBat, sva, GREAT, and more
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-\end_layout
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-
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-\end_deeper
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-\begin_layout Itemize
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-SICER, IDR, csaw, & GREAT to call ChIP-seq peaks genome-wide, perform differenti
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-al abundance analysis, and relate those peaks to gene expression
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-\end_layout
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-
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-\begin_layout Itemize
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-Promoter counts in sliding windows around each gene's highest-expressed
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- TSS to investigate coverage distribution within promoters
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-\end_layout
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-
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\begin_layout Subsection
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RNA-seq align+quant method comparison
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\end_layout
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