[README]: minor

README.org

@@ -34,7 +34,18 @@ There are some break changes :https://kzhang.org/SnapATAC2/changelog.html later
 
 [[./repo_figures/snATAC-seq_analysis_pipeline.jpg]]      
 ** Codes
-*** [[file:package/R/cembav2env.R][cembav2env.R]]: R env to store the metadata during analysis.
+*** Clustering
+    In total, we have implemented four-round iterative clustering.
+    See details in [[file:01.clustering][01.clustering]]
+*** Integration and annotation
+    We use Allen's scRNAseq data and their annotations for our data annotation.
+    See details in [[file:02.integration][02.integration]]
+*** Peak calling
+   We use macs2 with multiple stage filtering, especially use SPM >= 5
+   for filtering peaks.
+   See details in [[file:03.peakcalling][03.peakcalling]]
+*** Comments on some scripts:
+1. [[file:package/R/cembav2env.R][cembav2env.R]]: R env to store the metadata during analysis.
  |----------------+-------------------------------------------------------|
  | Enviorment     | Description                                           |
  |----------------+-------------------------------------------------------|
@@ -47,17 +58,6 @@ There are some break changes :https://kzhang.org/SnapATAC2/changelog.html later
  |----------------+-------------------------------------------------------|
  | Sa2PeakCalling | Peak calling meta data                                |
  |----------------+-------------------------------------------------------|
-*** Clustering
-    In total, we have implemented four-round iterative clustering.
-    See details in [[file:01.clustering][01.clustering]]
-*** Integration and annotation
-    We use Allen's scRNAseq data and their annotations for our data annotation.
-    See details in [[file:02.integration][02.integration]]
-*** Peak calling
-   We use macs2 with multiple stage filtering, especially use SPM >= 5
-   for filtering peaks.
-   See details in [[file:03.peakcalling][03.peakcalling]]
-