GMAP

##下载安装
wget http://research-pub.gene.com/gmap/src/gmap-gsnap-2023-04-28.tar.gz
cd gmap-2023-04-28
./configure --prefix=/home/lx_sky6/software/gmap-2023-04-28
make
make check
make install
export PATH=$PATH:/home/lx_sky6/software/gmap-2023-04-28/bin/

##建库
 gmap_build -D /home/lx_sky6/yt/20230106_baimaike/0105_YC_hifi/32_gmap  -d Rjup_genome /home/lx_sky6/yt/20230106_baimaike/0105_YC_hifi/10-EVM/4-evm-summary/genome.Rhodiola_juparensis.fa

-D 指定数据库的位置 -d 数据库前缀

##比对
gmap -t 40 -D /home/lx_sky6/yt/20230106_baimaike/0105_YC_hifi/32_gmap -d Rjup_genome -f 2 /home/lx_sky6/yt/20230106_baimaike/0105_YC_hifi/32_gmap/CYP711A.fasta > gene_gff3

提取

##转bed
/home/lx_sky6/software/miniconda3/envs/py_36/opt/transdecoder/util/gff3_file_to_bed.pl  gene_gff3 >bed
##提取基因cds和pep
gffread gene_gff3 -g /home/lx_sky6/yt/20230106_baimaike/0105_YC_hifi/10-EVM/4-evm-summary/genome.Rhodiola_juparensis.fa  -x cds.fa -y pep.fa