updated README

README.md

@@ -5,14 +5,21 @@ an aggregated report for pair-end reads, empowered by rmarkdown and plotly.
 
 ```bash
 $ cutqc.sh -h
-cutqc.sh in_read1.fq.gz in_read2.fq.gz out_report.html [cutadapt_option]
+cutqc.sh <cutqc> in_read1.fq.gz in_read2.fq.gz out_report.html [cutadapt_option]
 
-PLEASE REFER TO CUTADAPT AND FASTQC MANUAL ALSO.
+cutqc.sh <qc_only> in_read.fq.gz [output_report.html]
 
-Only pair-end gzipped input files are supported.
+cutqc has two valid subcommands:
+    cutqc:
+        Take pair-end inputs (R1.fq.gz and R2.fq.gz) and perform cutadapt in pair-end mode.
+        Fastqc will be performed both before and after trimming. The first three arguments
+        are mandatory and positional, all the following options will be parsed to cutadapt,
+        please refer to cutadapt manual for full option list.
 
-The first three arguments are mandatory and positional, all the other options
-followed will be parsed to cutadapt, please refer to cutadapt manual.
+    qc_only:
+        Take one single fastq file as input and perfom fastqc only.
+
+Please note only gzipped input file(s) are supported.
 ```
 
 ## Install