downstream

sinanugur · Aug 25, 2023 · 1ae400f · 1ae400f
1 parent 545b508
commit 1ae400f
Show file tree

Hide file tree

Showing 2 changed files with 12 additions and 3 deletions.
diff --git a/docs/downstream.rst b/docs/downstream.rst
@@ -16,21 +16,30 @@ For example, to load the Seurat object for the analysis with 10% MT threshold an
 
     library(Seurat)
     seurat_object <- readRDS("analyses/processed/percent_mt~10/resolution~0.8/sample_name.rds")
+    #integrated equivalent of this command is
+
+    seurat_object <- readRDS("analyses_integrated/processed/percent_mt~auto/resolution~0.8/integrated.rds")
+
+
+
 
 
 Annotation of cell types for this same dataset can be found in the `analyses/singler` directory.
 
 .. code-block:: R
 
     library(Seurat)
-    seurat_object <- readRDS("./analyses/singler/percent_mt~10/resolution~0.8/sample_name.rds")
+    singler_predictions <- readRDS("analyses/singler/percent_mt~10/resolution~0.8/sample_name.rds")
 
 
 Kraken2 predictions (metagenomics results) for this same dataset can be found in the `analyses/kraken` directory.
 
 .. code-block:: R
 
     library(Seurat)
-    seurat_object <- readRDS("./analyses/kraken/0_3/percent_mt~10/resolution~0.8/sample_name/microbiome-full-genus-level.rds")
+    kraken_predictions <- readRDS("analyses/kraken/0_3/percent_mt~10/resolution~0.8/sample_name/microbiome-full-genus-level.rds") #genus level predictions
+
+
+
 
 
diff --git a/docs/glossary.rst b/docs/glossary.rst
@@ -12,7 +12,7 @@ Here we explain some of the terminology related to Cellsnake and Seurat.
 
 **nCount_RNA** is the total number of molecules detected within a cell. You can access this plot under *technicals*.
 
-**mt.percent** Mitochondrial RNA percentage. We use "^[Mm][Tt]-" regex pattern to detect MT genes. Higher percentage of MT genes may suggest death cells.
+**mt.percent** Mitochondrial RNA percentage. We use "^[Mm][Tt]-" regex pattern to detect MT genes. Higher percentage of MT genes may suggest dead cells.
 
 **rp.percent** Ribosomal RNA percentage. We use "(?i)(^RP[SL])" regex pattern to detect ribosomal genes. Usually no filtering required for ribosomal genes.