├── AS-Quant_User_Manual.pdf ├── README.md ├── Result_Tsc1_null_Control_Vs_Tsc1_null_siU2af1.xlsx ├── as_quant.py ├── count_pvalue.py ├── hg19 ├── A3SS.csv ├── A5SS.csv ├── MXE.csv ├── RI.csv ├── SE.csv └── annotation.csv ├── hg38 ├── A3SS.csv ├── A5SS.csv ├── MXE.csv ├── RI.csv ├── SE.csv └── annotation.csv ├── make_plots.py ├── methods.py ├── mm10 ├── A3SS.csv ├── A5SS.csv ├── MXE.csv ├── RI.csv ├── SE.csv └── annotation.csv ├── preprocess.py ├── sample_input_mouse ├── group1 │ ├── s1.bam │ ├── s1.bam.bai │ └── s1 │ │ ├── chr1.bam │ │ ├── chr1.txt │ │ ├── chr10.bam │ │ ├── chr10.txt │ │ ├── chr11.bam │ │ ├── chr11.txt │ │ ├── chr12.bam │ │ ├── chr12.txt │ │ ├── chr13.bam │ │ ├── chr13.txt │ │ ├── chr14.bam │ │ ├── chr14.txt │ │ ├── chr15.bam │ │ ├── chr15.txt │ │ ├── chr16.bam │ │ ├── chr16.txt │ │ ├── chr17.bam │ │ ├── chr17.txt │ │ ├── chr18.bam │ │ ├── chr18.txt │ │ ├── chr19.bam │ │ ├── chr19.txt │ │ ├── chr2.bam │ │ ├── chr2.txt │ │ ├── chr3.bam │ │ ├── chr3.txt │ │ ├── chr4.bam │ │ ├── chr4.txt │ │ ├── chr5.bam │ │ ├── chr5.txt │ │ ├── chr6.bam │ │ ├── chr6.txt │ │ ├── chr7.bam │ │ ├── chr7.txt │ │ ├── chr8.bam │ │ ├── chr8.txt │ │ ├── chr9.bam │ │ ├── chr9.txt │ │ ├── chrX.bam │ │ ├── chrX.txt │ │ ├── chrY.bam │ │ └── chrY.txt └── group2 │ ├── s2.bam │ ├── s2.bam.bai │ └── s2 │ ├── chr1.bam │ ├── chr1.txt │ ├── chr10.bam │ ├── chr10.txt │ ├── chr11.bam │ ├── chr11.txt │ ├── chr12.bam │ ├── chr12.txt │ ├── chr13.bam │ ├── chr13.txt │ ├── chr14.bam │ ├── chr14.txt │ ├── chr15.bam │ ├── chr15.txt │ ├── chr16.bam │ ├── chr16.txt │ ├── chr17.bam │ ├── chr17.txt │ ├── chr18.bam │ ├── chr18.txt │ ├── chr19.bam │ ├── chr19.txt │ ├── chr2.bam │ ├── chr2.txt │ ├── chr3.bam │ ├── chr3.txt │ ├── chr4.bam │ ├── chr4.txt │ ├── chr5.bam │ ├── chr5.txt │ ├── chr6.bam │ ├── chr6.txt │ ├── chr7.bam │ ├── chr7.txt │ ├── chr8.bam │ ├── chr8.txt │ ├── chr9.bam │ ├── chr9.txt │ ├── chrX.bam │ ├── chrX.txt │ ├── chrY.bam │ └── chrY.txt └── samtools /AS-Quant_User_Manual.pdf: 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