From 06ef8be1b5ed40f493e82637e306dbfebcbd6a5b Mon Sep 17 00:00:00 2001
From: fiorini9 <110110777+fiorini9@users.noreply.github.com>
Date: Mon, 6 Nov 2023 10:02:01 -0500
Subject: [PATCH] Update step3_par.txt

---
 scrnabox.slurm/hto/pars/step3_par.txt | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/scrnabox.slurm/hto/pars/step3_par.txt b/scrnabox.slurm/hto/pars/step3_par.txt
index 2178219..59c266a 100644
--- a/scrnabox.slurm/hto/pars/step3_par.txt
+++ b/scrnabox.slurm/hto/pars/step3_par.txt
@@ -10,7 +10,7 @@ par_save_metadata= "yes"
 # Make sure that no other files/objects are present in the directory besides Seurat RDS objects. 
 # Uncomment the line to activate the parameter
 ############################################################################
-#par_seurat_object= "/path/to/seurat/object"
+#par_seurat_object= "/path/to/directory/containing/seurat/object"
 
 
 ############################################################################
@@ -19,13 +19,21 @@ par_save_metadata= "yes"
 # L = lower bound threshold
 # R = upper bound threshold
 ############################################################################
+## minimum number of unique RNA transcripts
 par_nFeature_RNA_L= 50
+## maximum number of unique RNA transcripts
 par_nFeature_RNA_U= 6000
+## minimum number of total RNA transcripts
 par_nCount_RNA_L= 200
+## maximum number of total RNA transcripts
 par_nCount_RNA_U= 20000
+## Minimum mitochondrial RNA percentage
 par_mitochondria_percent_L= 0
+## Maximum mitochondrial RNA percentage
 par_mitochondria_percent_U= 50
+## Minimum ribosomal RNA percentage
 par_ribosomal_percent_L= 0
+## Maximum ribosomal RNA percentage
 par_ribosomal_percent_U= 100