Update hisat-3n.md

docs/_pages/hisat-3n.md

@@ -169,15 +169,15 @@ Generate 3N-conversion-table with `hisat-3n-table`:
 
 * `--ref <refFile>`  
   The reference genome file (FASTA format) for generating HISAT-3N index.
+
+* `--output-name <outputFile>`  
+  Filename to write 3N-conversion-table (tsv format) to.  By default, table is written to the “standard out” or “stdout” filehandle (i.e. the console).
 
 * `--base-change <char1,char2>`  
   The base-change rule. User should enter the exact same `--base-change` arguments in hisat-3n.
   For example, please enter `--base-change C,T` for bisulfite sequencing reads.
 
 #### Input options
-* `--output-name <outputFile>`  
-  Filename to write 3N-conversion-table (tsv format) to.  By default, table is written to the “standard out” or “stdout” filehandle (i.e. the console).
-
 * `-u/--unique-only`  
   Only count the unique aligned reads into 3N-conversion-table.
 
@@ -187,9 +187,6 @@ Generate 3N-conversion-table with `hisat-3n-table`:
 * `-c/--CG-only`  
   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.
-
 * `--added-chrname`  
   Please add this option if you use `--add-chrname` during `hisat-3n` alignment. 
   During `hisat-3n` alignment, the prefix "chr" is added in front of chromosome name and shows on SAM output, when user choose `--add-chrname`.
@@ -202,10 +199,13 @@ Generate 3N-conversion-table with `hisat-3n-table`:
   `hisat-3n-table` cannot find the chromosome name on reference because it has no "chr" prefix. This option is to help `hisat-3n-table`
   find the matching chromosome name on reference file. The 3n-table provides the same chromosome name as SAM file.
 
+#### Other options:
+* `-p/--threads <int>`  
+  Launch `int` parallel threads (default: 1) for table building.
+
 * `-h/--help`  
   Print usage information and quit.
 
-
 #### Examples:
     # 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