From c6ea913129831383bc116998e1de000c333674ac Mon Sep 17 00:00:00 2001
From: Lorena Pantano <lorena.pantano@gmail.com>
Date: Tue, 17 Dec 2024 10:15:49 -0500
Subject: [PATCH] Update atacseq notes

---
 docs/pipelines.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/docs/pipelines.md b/docs/pipelines.md
index abbd00c..4938c8f 100644
--- a/docs/pipelines.md
+++ b/docs/pipelines.md
@@ -36,6 +36,9 @@ NFR peaks `nf-core-atac-seq_shift_NFR`:
   - `--minFragmentLength 0`
   - `--maxFragmentLength 120`
 
+**Note**: Recommendation to check the fragment length distribution after the run to make sure you're capturing the NFRs.
+**Note**: We don't need the MN(180, 247), DN (315, 473) and TN (558, 615), unless it's a specific case where we are looking at global shifts in accessibility
+
 ## Nextflow in Seqera platform
 
 - Create an user here: https://cloud.seqera.io/login