From 61df3d25f0f2ba5bbbe73bd602c6f6b7ecf076c9 Mon Sep 17 00:00:00 2001
From: Jessica Mattick <19544292+jmattick@users.noreply.github.com>
Date: Fri, 21 Oct 2022 15:53:19 -0500
Subject: [PATCH] Add cell calling page (#41)

Co-authored-by: Jessica Mattick <jmattick@pacificbiosciences.com>
---
 docs/umi/cell-calling.md   | 18 ++++++++++++++++++
 docs/umi/isoseq-correct.md |  1 +
 2 files changed, 19 insertions(+)
 create mode 100644 docs/umi/cell-calling.md

diff --git a/docs/umi/cell-calling.md b/docs/umi/cell-calling.md
new file mode 100644
index 0000000..8e7afc9
--- /dev/null
+++ b/docs/umi/cell-calling.md
@@ -0,0 +1,18 @@
+---
+layout: default
+parent: Single cell
+title: Cell Calling
+nav_order: 6
+---
+
+## Cell Calling Documentation
+
+There are two available methods for determining real cells.
+
+### Knee Finding Method (default)
+
+The knee finding method is the default method for determining real cells. It works by identifying the knee of the barcode rank plot based on [*UMI-tools*](https://github.com/CGATOxford/UMI-tools). 
+
+### Percentile Method
+
+The percentile method approximates real cells based on a percentile cutoff of UMI counts per cell. This method first identifies the X percentile (default 99) of UMI counts per cell, then applies a multiplier of X 10 to generate a cutoff threshold of UMI counts for real cells. 
diff --git a/docs/umi/isoseq-correct.md b/docs/umi/isoseq-correct.md
index 554e286..f3c3d45 100644
--- a/docs/umi/isoseq-correct.md
+++ b/docs/umi/isoseq-correct.md
@@ -39,6 +39,7 @@ For each input HiFI read containing a 10x cell barcode:
  -  If no candidates were found, the barcode is unchanged, and the read is marked as failing.
 
 In addition, "real cells" will be marked with `rc` tag after this step, which will be used by `isoseq3 groupdedup`.
+For details on real cell calling, visit the [cell calling](https://isoseq.how/umi/cell-calling.html) page.
 
 ### When would a user call this tool?