Update README.md

README.md

@@ -14,6 +14,110 @@ Unzip ASM-detector.zip file. Executable files are under bin folder.
 To add ASM-detector to $PATH, [check here](http://askubuntu.com/questions/109381/how-to-add-path-of-a-program-to-path-environment-variable)
 
 ## 3 Demo
+[Download demo data](demo.zip)
+
+Demo folder structure:
+```
+.
+├── chr8.fa
+└── TRAPPC9_ads_adipose.sam
+```
+All following command are executed in demo folder. Assuming ASM-Detector required softwares are setup properly(added to $PATH). You can also execute commands through relative path, e.g. ../bin/cpmr, which assume bin folder is in the same level of demo folder.
+
+## 3.1 cpmr: generate candidate ASM regions
+```
+>cpmr -m TRAPPC9_ads_adipose.sam -r chr8.fa -mcc 4 -mic 5 -mir 10 -p 0.3 --format sam -o TRAPPC9 -pe
+Load refChr chr8-0-146364021 with 1309135 RefCpGs. Complete in 2.412000 s
+Load 4601 Mapped Reads. Complete in 0.249000 s
+```
+After execution, demo folder looks like:
+```
+.
+├── chr8.fa
+├── TRAPPC9
+│   ├── chr8-141108112-141109094.mappedreads
+│   ├── chr8-141109226-141110677.mappedreads
+│   ├── chr8-141110686-141111080.mappedreads
+│   ├── CPMR.bed
+│   └── CPMR.report
+└── TRAPPC9_ads_adipose.sam
+```
+## 3.2 asmd: detect ASM regions
+```
+>asmd -i TRAPPC9 -mic 5 -p 100 -t 8 -o TRAPPC9_result
+```
+After execution, demo folder looks like:
+```
+.
+├── chr8.fa
+├── TRAPPC9
+│   ├── chr8-141108112-141109094.mappedreads
+│   ├── chr8-141109226-141110677.mappedreads
+│   ├── chr8-141110686-141111080.mappedreads
+│   ├── CPMR.bed
+│   └── CPMR.report
+├── TRAPPC9_ads_adipose.sam
+└── TRAPPC9_result
+    ├── chr8-141108112-141109094.mappedreads.detected
+    ├── chr8-141108112-141109094.mappedreads.groups.aligned
+    ├── chr8-141109226-141110677.mappedreads.detected
+    ├── chr8-141109226-141110677.mappedreads.groups.aligned
+    ├── chr8-141110686-141111080.mappedreads.detected
+    ├── chr8-141110686-141111080.mappedreads.groups.aligned
+    └── detection.summary
+```
+## 3.3 mfig: generate methylation figure base on aligend reads file.
+```
+>mfig  -i TRAPPC9_result/chr8-141109226-141110677.mappedreads.groups.aligned -p 141109990 -a T-G -s 22
+```
+Output is in the same folder of input file with file name extension ".compact.eps".
+Example: chr8-141109226-141110677.mappedreads.groups.aligned.compact.eps
+
+# 4.Interface
+## 4.1 cpmr:
+```
+usage: cpmr [options]
+    --format <arg>   specify format of input: mappedread, sam
+ -m <arg>            MappedRead File (Required)
+ -mcc <arg>          Minimum adjacent CpG coverage (Required)
+ -mic <arg>          Minimum interval CpG number (Required)
+ -mir <arg>          Minimum interval read number (Required)
+ -o <arg>            Output Path (Required)
+ -p <arg>            Partial methylation threshold (Required)
+ -pe                 Pair end mode (Optional)
+ -r <arg>            Reference File (Required)
+```
+## 4.2 asmd:
+```
+usage: asmd [options]
+ -i <arg>     Input intervals folder or interval file name (Required)
+ -mic <arg>   Minimum interval CpG number (Required)
+ -o <arg>     output folder. Will be create if not exist (Required)
+ -p <arg>     Time of random permutation (Required)
+ -t <arg>     Thread number to call the program (Required)
+ ```
+## 4.3 mfig:
+```
+usage: mfig [options]
+ -a <arg>   allele pair. E.g. A-G
+ -i <arg>   input grouped read file
+ -p <arg>   SNP position
+ -s <arg>   font size
+```
+
+# 5.Output
+## 5.1 cpmr output
+### CPMR.bed
+Bed file contains every CPMR regions and their read count/cpg count.
+### Individual CPMR region read file
+Contains reference sequnece and reads with columns(ref,strand,start,end,sequence,ID)
+## 5.2 asmd output
+### detection.summary
+Bed file contains each ASM region detected.
+### .detected file
+Contains p-value, average methylation information and covered read count(in bracket) of each CpG site in every groups.
+### .groups.aligned file
+Similar to CPMR region file. However reads in this file are aligned by coordinates and separated into groups for visulization purpose.
 
 
 ## Citation