Merge pull request DaehwanKimLab#319 from DaehwanKimLab/3ndoc

update hisat-3n manual for --CG-only
mourisl · Aug 17, 2021 · c54f3d4 · c54f3d4
2 parents 6cf38fa + 64a5f7b
commit c54f3d4
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/docs/_pages/hisat-3n.md b/docs/_pages/hisat-3n.md
@@ -186,7 +186,7 @@ Generate 3N-conversion-table with `hisat-3n-table`:
   Only count the multiple aligned reads into 3N-conversion-table.
 
 * `-c/--CG-only`  
-  Only count the CpG island in reference genome. This option is designed for bisulfite sequencing reads.
+  Only count the CpG sites in reference genome. This option is designed for bisulfite sequencing reads.
 
 * `-p/--threads <int>`  
   Launch `int` parallel threads (default: 1) for table building.
@@ -211,7 +211,7 @@ Generate 3N-conversion-table with `hisat-3n-table`:
     # Generate the 3N-conversion-table for bisulfite sequencing data:  
       hisat-3n-table -p 16 --alignments sorted_alignment_result.sam --ref genome.fa --output-name output.tsv --base-change C,T
 
-    # Generate the 3N-conversion-table for TAPS data and only count base in CpG island and uniquely aligned:  
+    # Generate the 3N-conversion-table for TAPS data and only count base in CpG site and uniquely aligned:  
       hisat-3n-table -p 16 --alignments sorted_alignment_result.sam --ref genome.fa --output-name output.tsv --base-change C,T --CG-only --unique-only
 
     # Generate the 3N-conversion-table for bisulfite sequencing data from sorted BAM file: