From 1b57f40e5a5419f8288ac9d67d45ecc559d922d3 Mon Sep 17 00:00:00 2001 From: Xu lab <64727159+Xu-Lab-WHU@users.noreply.github.com> Date: Wed, 2 Sep 2020 16:02:31 +0800 Subject: [PATCH] Update README.md update options --- README.md | 40 +++++++++++++++++++++++++++++++++++++++- 1 file changed, 39 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 73073c8..6d19942 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,40 @@ -# 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 -s -b -c -i -r -t -rl +``` +### 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***