$ pip install GetTsite

$ GetTss -h usage: GetTss --database ucsc --gtffile hg19.ncbiRefSeq.gtf --tssfile testTSS.bed Get gene TSS site and export bed format from GTF annotation file. optional arguments: -h, --help show this help message and exit -v, --version show program's version number and exit  -d {ucsc,ensembl,gencode}, --database {ucsc,ensembl,gencode}  which annotation database you choose. (default="ensembl")  -g GTFFILE, --gtffile GTFFILE  input your GTF file. (ucsc/ensembl/gencode)  -t TSSFILE, --tssfile TSSFILE  output your TSS file. (test-TSS.bed)  Thank your for your support, if you have any questions or suggestions please contact me: 3219030654@stu.cpu.edu.cn.

$ GetTss -d ucsc -g hg19.ncbiRefSeq.gtf -t ucsc-TSS.bed Your job is starting, please wait! You GTF file have: 104178 transcripts. Your task has down! $ head -n 3 ucsc-TSS.bed chrMT 16023 16024 TRNP . - chrMT 15887 15888 TRNT . + chrMT 14746 14747 CYTB . +

$ GetTss -d gencode -g gencode.v19.annotation.gtf -t test-TSS.bed Your job is starting, please wait! You GTF file have: 57820 genes. Your task has down! $ head -n 3 test-TSS.bed chr1 11868 11869 ENSG00000223972.4 . + chr1 29806 29807 ENSG00000227232.4 . - chr1 29553 29554 ENSG00000243485.2 . +

$ GetTes -d ucsc -g hg19.ncbiRefSeq.gtf -t ucsc-TSS.bed $ GetTes -d gencode -g gencode.v19.annotation.gtf -t test-TES.bed

$ computeMatrix reference-point -S normal.bw treat.bw \ -R myTSS.bed \ --referencePoint center \ -a 3000 -b 3000 -p 25 \ -out matrix.tab.gz

$ plotProfile -m matrix.tab.gz \ -out profile.pdf \ --perGroup \ --plotTitle 'test profile'