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 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 &

Output :

Running tmp file can find in design.dot.library/library.results/ directoy.

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. (2020) Defective Minor Spliceosomes Induce SMA-associated phenotypes through Sensitive Intron-Containing Neural Genes in Drosophila. Nature Communication. 11:5608, doi: 10.1038/s41467-020-19451-z.