Update README.md

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README.md

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-# UnusedIndex
+# UnusedIndex 
+**VERSION 1.0.0**
+
 Bioinformatic tool to measure the Unused Index of each Splice Site from RNA-seq
+
+    Caculate Splice Site UnsedIndex
+
+## Usage:
+```
+perl $0 -a <FILE> -s <LIST> -b <LIST> -c <STRINGS> -i <INT> -r <INT> -t <INT> -rl <INT>
+```
+### Options: 
+        
+        -a,--annotation   annotation gtf file.
+        -s,--sam          sam file by mapping and be split by comma.
+                          e.g.: 
+                          wt-1.sam,wt-2.sam,RNAi-1.sam,RNAi-2.sam
+        -b,--bam          bam file and be split by comma.
+        -n,--sampleName   sample name list. 
+        -c,--compare      compare wt and mut. 
+                          e.g.: 
+                          larva_rep1,mut1;larva_rep1,mut2;larva_rep2,mut1;larva_rep2,mut2
+        -i,--intronL      the minimum intron length. (defaut:15)
+        -r,--suportReads  the minimum reads which suport the nonvel 
+                          junction. (defaut:20)
+        -t,--tolerable    the maximum location changes nearby the 
+                          correct dot. (defaut:2)
+        -rl               the maximun library useful region.(defaut is 40)
+        -h,--help
+
+## Example running :
+```perl
+perl unused.index.pl -a test.data/dmel-all-r6.23.gtf \
+          -s test.data/wt-1.sam,test.data/wt-2.sam,test.data/mut-1.sam,test.data/mut-2.sam \
+          -b test.data/wt-1.bam,test.data/wt-2.bam,test.data/mut-1.bam,test.data/mut-2.bam \
+          -n wt-1,wt-2,mut-1,mut-2 -c wt-1,mut-1:wt-1,mut-2:wt-2,mut-1:wt-2,mut-2 \
+          -i 15 -r 20 -t 2 -rl 40 > 2019.7.31 &
+```
+## Please Cite :
+Liang Li, Zhan Ding, Ting-Lin Pang, Bei Zhang, Chen-Hui Li, An-Min Liang, Yu-Ru Wang, Yu Zhou, Yu-Jie Fan, and Yong-Zhen Xu. **Defective Minor Spliceosomes Induce SMA-associated phenotypes through Sensitive Intron-Containing Neural Genes in Drosophila.** *Nature Communication.* ***In Press***