From dfe27fa04a40e38aba59773fa6f7f6ff529edb42 Mon Sep 17 00:00:00 2001
From: Giulio Formenti <47462635+gf777@users.noreply.github.com>
Date: Wed, 17 Mar 2021 21:45:09 -0400
Subject: [PATCH] Update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 7502b0d..3b3204a 100644
--- a/README.md
+++ b/README.md
@@ -29,7 +29,7 @@ As a rule of thumb, the `-peak` should be:
 Optionally, a custom lookup table of kmer multiplicities with fitted copy numbers and probabilities can be provided (`-lookup`). The lookup table is generated when running our modified version of [Genomescope 2.0](/~https://github.com/gf777/genomescope2.0). This is recommended, and can significantly improve the accuracy of all analyses:
 
 ```
-Rscript genomescope.R <kmer_histogram> <k_size> <output_folder> --fitted_hist [ploidy] [verbose]
+Rscript genomescope.R -h <kmer_histogram>  -k <k_size> -o <output_folder> --fitted_hist [ploidy] [verbose]
 kmer_histogram  tab-delimited, 2-column file with (same as for Genomescope2, usually generated by meryl hist, or jellyfish)
 k_size          kmer length used for the histogram
 ploidy          haploid/diploid (default = 2)