From 15542ebfd3e07464c994e04156804ea0dbe82622 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 16 Sep 2019 11:04:41 -0500
Subject: [PATCH] Update index.md
---
docs/index.md | 20 ++++++++++----------
1 file changed, 10 insertions(+), 10 deletions(-)
diff --git a/docs/index.md b/docs/index.md
index 745e664..2532ad9 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -41,22 +41,22 @@ To Run:
* *'hg19_and_mm10-1.2.0'* = Human GRCh37 (hg19) + Mouse GRCm38 (mm10) release 84
* *'ercc92-1.2.0'* = ERCC.92 Spike-In
* **expect cells**
- * Expected number of recovered cells.
- * guides cellranger in it's cutoff for background/low quality cells
- * as a guide it doesn't have to be exact
- * 0-10000
- * if --expextedCells is used then --forceCells is not necessary
- * only used if force cells is not entered or set to 0
- * **force cells**
- * Force pipeline to use this number of cells, bypassing the cell detection algorithm. Use this if the number of cells estimated by Cell Ranger is not consistent with the barcode rank plot. A value of 0 ignores this option. Any value other than 0 overrides expect-cells.
+ * Expected number of recovered cells.
+ * guides cellranger in it's cutoff for background/low quality cells
+ * as a guide it doesn't have to be exact
* 0-10000
- * if force cells is used then expected cells is not necessary and is ignored
+ * if --expextedCells is used then --forceCells is not necessary
+ * only used if force cells is not entered or set to 0
+ * **force cells**
+ * Force pipeline to use this number of cells, bypassing the cell detection algorithm. Use this if the number of cells estimated by Cell Ranger is not consistent with the barcode rank plot. A value of 0 ignores this option. Any value other than 0 overrides expect-cells.
+ * 0-10000
+ * if force cells is used then expected cells is not necessary and is ignored
* **chemistry version**
* 10x single cell gene expression chemistry version (only used in cellranger version 3.x).
* setting to auto will attempt to autodetect from the detected cycle strategy in the fastq's
* chemistry version is only used if cellranger version is > 2.x
* cellranger version 2.1.1 can only read chemistry version less than or equal to two (2)
- * **cellranger version**
+ * **cellranger version**
* 10x cellranger version.
* cellranger version 2.1.1 can only read chemistry version less than or equal to two (2)
--
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