建立索引

STAR  --runMode genomeGenerate \\
    --genomeDir ref \\
    --runThreadN 10 \\
    --genomeFastaFiles reference.fa\\
    --sjdbGTFfile reference.gtf

转录组STAR比对

STAR \\
    --genomeDir STAR \\
    --runThreadN 10 \\
    --readFilesIn /home/liuli/geneomic/GDDR1694-1-18例地衣RNA-Seq测序/GDDR1694-1_order_5/R1/_Lh1-1_S110_L007_R1_001.fastq,/home/liuli/geneomic/GDDR1694-1-18例地衣RNA-Seq测序/GDDR1694-1_order_5/R2/_Lh1-1_S110_L007_R2_001.fastq \\
    --outFileNamePrefix lh_1-1_ \\
    --outSAMtype BAM SortedByCoordinate \\
    --outBAMsortingThreadN 10 \\
    --outSAMstrandField intronMotif \\
    --outFilterIntronMotifs RemoveNoncanonical

https://blog.csdn.net/u012110870/article/details/102804525

BRAKER

singularity exec -B /public1/home/t0s000552/:/public1/home/t0s000552/ braker3.sif braker.pl \\
--genome=/public1/home/t0s000552/rna-seq/hic-final-green.fasta.masked \\ ##写绝对路径，不能识别~
--species=hic-green \\ 
--bam=/public1/home/t0s000552/rna-seq/hicAligned.sortedByCoord.out.bam \\ 
--softmasking \\
--workingdir=/public1/home/t0s000552/green/braker3 \\
--threads 30 \\
--gff3 \\
--AUGUSTUS_CONFIG_PATH=/public1/home/t0s000552/miniforge-pypy3/pkgs/augustus-3.5.0-pl5321h700735d_3/config/ \\ ##config地址
--GENEMARK_PATH=/public1/home/t0s000552/green/braker3/gmes_petap.pl \\ ##把gmes_petap.pl写入绝对路径

如果出现singularity: command not found的话，加上/usr/bin/singularity绝对路径

#for i in $(ls *fna); do /usr/bin/singularity exec ../braker3.sif braker.pl --genome=$i --esmode --gff3 --AUGUSTUS_CONFIG_PATH=~/liuli/anaconda3/envs/python2.7/bin/augustus --GENEMARK_PATH==~/liuli/anaconda3/envs/python2.7/bin/gmes_petap.pl --threads 48 --workingdir=/home/liuli/liuli/backup/geneomic/BRAKER-master/new/BRAKER-master/lichen/${i}_2 --fungus; done