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SEACR_1.1 Update #6

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SEACR_1.1 Update #6

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21 changes: 14 additions & 7 deletions README.md
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Expand Up @@ -9,9 +9,16 @@ Meers MP, Bryson TD, Henikoff S. A streamlined protocol and analysis pipeline fo

Direct link: https://www.biorxiv.org/content/10.1101/569129v2

## Recent changes

### v1.1
- Changed "union" and "AUC" modes to "relaxed" and "stringent" modes, respectively.
- Removed maximum signal threshold from "relaxed" mode and replaced it with an alternate total signal threshold that uses the point halfway between the knee and the peak of the total signal curve as described in the manuscript text. This change improves performance at high read depth.
- Implemented alternate threshold test that searches for any thresholds that come within 95% of the optimal threshold. This change avoids spurious thresholds that are overselective in some datasets.

## Usage:

bash SEACR_1.0.sh experimental bedgraph [control bedgraph | numeric threshold] ["norm" | "non"] ["union" | "AUC"] output prefix
bash SEACR_1.1.sh experimental bedgraph [control bedgraph | numeric threshold] ["norm" | "non"] ["relaxed" | "stringent"] output prefix

## Description of input fields:

Expand All @@ -21,7 +28,7 @@ Field 2: Control (IgG) data bedgraph file to generate an empirical threshold for

Field 3: “norm” denotes normalization of control to target data, “non” skips this behavior. "norm" is recommended unless experimental and control data are already rigorously normalized to each other (e.g. via spike-in).

Field 4: “union” forces implementation of a maximum signal threshold in addition to the total signal threshold, and corresponds to the “union” mode described in the text, whereas “AUC” avoids this behavior, and corresponds to “AUC only” mode.
Field 4: “relaxed” uses a total signal threshold between the knee and peak of the total signal curve, and corresponds to the “relaxed” mode described in the text, whereas “stringent” uses the peak of the curve, and corresponds to “stringent” mode.

Field 5: Output prefix

Expand Down Expand Up @@ -52,11 +59,11 @@ Field 6: Region representing the farthest upstream and farthest downstream bases

## Examples:

bash SEACR_1.0.sh target.bedgraph IgG.bedgraph norm AUC output
Calls enriched regions in target data using normalized IgG control track with AUC threshold
bash SEACR_1.1.sh target.bedgraph IgG.bedgraph norm AUC output
Calls enriched regions in target data using normalized IgG control track with stringent threshold

bash SEACR_1.0.sh target.bedgraph IgG.bedgraph non union output
Calls enriched regions in target data using non-normalized IgG control track with AUC and max signal thresholds
bash SEACR_1.1.sh target.bedgraph IgG.bedgraph non union output
Calls enriched regions in target data using non-normalized IgG control track with relaxed threshold

bash SEACR_1.0.sh target.bedgraph 0.01 non AUC output
bash SEACR_1.1.sh target.bedgraph 0.01 non AUC output
Calls enriched regions in target data by selecting the top 1% of regions by AUC