Update step5_par.txt

neurobioinfo · Nov 10, 2023 · 6aaa21d · 6aaa21d
1 parent 91145e7
commit 6aaa21d
Showing 1 changed file with 20 additions and 17 deletions.
diff --git a/scrnabox.slurm/hto/pars/step5_par.txt b/scrnabox.slurm/hto/pars/step5_par.txt
@@ -22,49 +22,52 @@ par_one_seurat= "no"
 ############################################################################
 # If you have multiple Seurat objects, choose whether you want to integrate or merge the objects
 ############################################################################
+## integrate Seurat objects
 par_integrate_seurat= "yes"
-par_merge_seurat= "no"
-
 
-############################################################################
-# Parameters for integration
-############################################################################
-## Which dimensions to use from the CCA to specify the neighbour search space
-par_FindIntegrationAnchors_dim= 25 
+## merge Seurat objects
+par_merge_seurat= "no"
 
 
 ############################################################################
 # Parameters for normalization and scaling
-# even if you opt to skip integration, adjust the following parameters 
+# Even if you opt to skip integration, adjust the following parameters 
 ############################################################################
-## Assay to perform normalization and scaling. For most use cases this will be RNA
+## Assay to perform normalization and scaling (prior to integration). For most use cases this will be RNA
 par_DefaultAssay= "RNA"
 
 ## Normalization method
 par_normalization.method= "LogNormalize"
 
-## Scale factor for normalization
+## Scale factor
 par_scale.factor= 10000
 
+
+############################################################################
+# Parameters for integration
+############################################################################
 ## Method for detecting top variable features. vst, mean.var.plot (mvp), dispersion (disp)
 par_selection.method= "vst"
 
-## Number of features to select as top variable features
+## Number of features to select as top variable features for integration
 par_nfeatures= 2500
 
+## Which dimensions to use from the CCA to specify the neighbour search space
+par_FindIntegrationAnchors_dim= 25 
+
 
 ############################################################################
 # Parameters for linear dimensional reduction
 # even if you opt to skip integration, adjust the following parameters 
 ############################################################################
-## The number of neighbouring points used in local approximations of manifold structure
-par_RunUMAP_n.neighbors= 65
-
 ## Total Number of PCs to compute and store for RunPCA
 par_RunPCA_npcs= 30
 
-##  Which dimensions to use as input features for RunUMAP
-par_RunUMAP_dims= 30
+## Which dimensions to use as input features for RunUMAP
+par_RunUMAP_dims= 25
+
+## The number of neighbouring points used in local approximations of manifold structure.
+par_RunUMAP_n.neighbors= 45
 
-## whether or not to perform JackStraw computation. This computation takes a long time.
+## Whether or not to perform JackStraw computation. This computation takes a long time.
 par_compute_jackstraw= "no"