From 40952c40aa4aaf8b403a44af6e1202a9a8ee8375 Mon Sep 17 00:00:00 2001
From: Jayoung Kim Ryu <jayoung_ryu@g.harvard.edu>
Date: Wed, 6 Mar 2024 22:24:52 -0800
Subject: [PATCH] Add bean-count documentation

---
 README.md | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/README.md b/README.md
index eead4ed..787b343 100644
--- a/README.md
+++ b/README.md
@@ -80,6 +80,16 @@ bean-count-samples \
   -t 12                     `# number of threads` \
   --name my_sorting_screen  `# name of this sample run`
 ```
+```python
+bean-count \
+  --R1 read1.fq[.gz]
+  --R2 read2.fq[.gz]
+  -b A                      `# base that is being edited (A/G)` \
+  -f sgRNA_info_table.csv   `# sgRNA information` \
+  -o .                      `# output directory` \
+  -r                        `# read edit/allele information from reporter` \
+  --name my_sample  `# name of this sample run`
+```
 
 ### Input file format
 #### 1. gRNA_library.csv