From bc97d581141cb2855bfb34e74f1fda22e7eb27fe Mon Sep 17 00:00:00 2001
From: Mia Croiset <mia.croiset@ens-lyon.fr>
Date: Wed, 27 Mar 2024 14:52:11 +0100
Subject: [PATCH] fix argument name for filter_pcr and cutsite_seed default
 value

---
 docs/hicstuff_usage.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/docs/hicstuff_usage.md b/docs/hicstuff_usage.md
index 07abb2c..efb86bb 100644
--- a/docs/hicstuff_usage.md
+++ b/docs/hicstuff_usage.md
@@ -133,7 +133,7 @@ Default: for_vs_rev
 ### `--cutsite_seed`
 
 Minimum size of a fragment (i.e. seed size used in mapping as reads smaller won't be mapped.)
-Default: 0
+Default: 20
 
 ```bash
 --cutsite_seed '[Size of fragment]'
@@ -375,11 +375,11 @@ Name of distance law table plot if hicstuff_distance_plot is true. Default: dist
 --hicstuff_distance_out_plot '[Name of distance law plot file]'
 ```
 
-#### `--hicstuff_filter_pcr`
+#### `--filter_pcr`
 If true, PCR duplicates will be filtered based on genomic positions Pairs where both reads have exactly the same coordinates are considered duplicates and only one of those will be conserved. Default: false
 
 ```bash
---hicstuff_filter_pcr
+--filter_pcr
 ```
 > :warning: **Warning**: if true, `--filter_pcr_picard` **must** be false
 
@@ -392,7 +392,7 @@ Name of pair file after PCR filtering. Default: 'valid_idx_pcrfree.pairs'
 
 #### `--filter_pcr_picard`
 
-If specified, duplicate reads are filtered using PICARD MarkDuplicate method. If true, `--hicstuff_filter_pcr` **must** be false. Default:'false'
+If specified, duplicate reads are filtered using PICARD MarkDuplicate method. If true, `--filter_pcr` **must** be false. Default:'false'
 
 ```bash
 --filter_pcr_picard
-- 
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