Update seurat defaults

Author: bbimber

singlecell/src/org/labkey/singlecell/pipeline/singlecell/FilterRawCounts.java

@@ -25,13 +25,13 @@ public Provider()
                     }}, 0, "nCount_RNA.low", false),
                     SeuratToolParameter.create("nCountRnaHigh", "Max UMI Count", "Cells with UMI counts above this value will be discarded", "ldk-integerfield", new JSONObject(){{
                         put("minValue", 0);
-                    }}, 20000, "nCount_RNA.high", false),
+                    }}, 30000, "nCount_RNA.high", false),
                     SeuratToolParameter.create("nCountFeatureLow", "Min Feature Count", "Cells with unique feature totals below this value will be discarded", "ldk-integerfield", new JSONObject(){{
                         put("minValue", 0);
-                    }}, 200, "nFeature.low", false),
+                    }}, 150, "nFeature.low", false),
                     SeuratToolParameter.create("nCountFeatureHigh", "Max Feature Count", "Cells with unique feature totals above this value will be discarded", "ldk-integerfield", new JSONObject(){{
                         put("minValue", 0);
-                    }}, 5000, "nFeature.high", false),
+                    }}, 7500, "nFeature.high", false),
                     SeuratToolParameter.create("pMitoLow", "Min Percent Mito", "Cells percent mitochondrial genes below this value will be discarded", "ldk-numberfield", new JSONObject(){{
                         put("minValue", 0);
                         put("maxValue", 1);

singlecell/src/org/labkey/singlecell/pipeline/singlecell/PrepareRawCounts.java

@@ -39,10 +39,10 @@ public Provider()
                     }}, 0.001),
                     SeuratToolParameter.create("maxAllowableCells", "Max Cells Allowed", "If more than this many cells are predicted by EmptyDrops, the job will fail", "ldk-integerfield", new JSONObject(){{
                         put("minValue", 0);
-                    }}, 20000),
+                    }}, 35000),
                     SeuratToolParameter.create("minAllowableCells", "Min Cells Allowed", "If fewer than this many cells are predicted by EmptyDrops, the job will fail", "ldk-integerfield", new JSONObject(){{
                         put("minValue", 0);
-                    }}, 1500),
+                    }}, 500),
                     SeuratToolParameter.create("useEmptyDropsCellRanger", "Use emptyDropsCellRanger", "If checked, this will run emptyDropsCellRanger instead of emptyDrops", "checkbox", null, false),
                     SeuratToolParameter.create("nExpectedCells", "# Expected Cells", "Only applied if emptyDropsCellRanger is selected. Passed to n.expected.cells argument", "ldk-integerfield", new JSONObject(){{
                         put("minValue", 0);