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example.readme
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###1.For annotaion
python3 /public/source/share/zcs/v20210402_1/TransAnnot.py -c /public/source/share/zcs/v20210402_1/759133C.config
python3 /public/source/share/zcs/v20210402_1/TransAnnot.py -c /public/source/share/zcs/v20210402_1/759133N.config
###2.For gene fusion
Rscript TAGET_fusion_2-3_ajust.r -j Jin_fusion_select.py -e STAT_select.py -l 759133C.fa.minimap2.bed -s 759133C.fa.hisat2.bed -a 759133N.anno.tmp.stat -t hg38.gtf -f 759133C.fa -n name_759133C -o ./output
###3.For DIU analysis
###1) generate expression file
python3 fa2exp.py -f /public/source/share/zcs/ISOtect/final1/fa/759133C.fa -i 759133C.annot -o /public/source/share/zcs/ISOtect/final1/fa/759133C/ -p /public/source/share/zcs/ISOtect/final1/fa/759133C/
python3 fa2exp.py -f /public/source/share/zcs/ISOtect/final1/fa/759133N.fa -i 759133N.annot -o /public/source/share/zcs/ISOtect/final1/fa/759133N/ -p /public/source/share/zcs/ISOtect/final1/fa/759133N/
###2)this step can generate merge file of tumor and nomral and will compute differential gene expression by using DEG-Seq
python script.py input.config
###3) compute DIU gene
python expression_V1.py -t 759133_merge.trans.exp.knwon -o 759133
##########
reference genome can be downlaod from https://disk.pku.edu.cn:443/link/1F62976F65C4EA81C4C06A05E245049D